Variant report

Variant	rs746429
Chromosome Location	chr11:65417434-65417435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65417318-65417472	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:65417197-65417698	HL-60	blood:	n/a	n/a
3	POLR2A	chr11:65413726-65418689	K562	blood:	n/a	n/a
4	POLR2A	chr11:65416453-65424304	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65311946..65314284-chr11:65416620..65419973,3	MCF-7	breast:
2	chr11:65379754..65386537-chr11:65415130..65425067,26	MCF-7	breast:
3	chr11:65416969..65422455-chr11:65556396..65561611,5	MCF-7	breast:
4	chr11:65342372..65345081-chr11:65416714..65420575,4	MCF-7	breast:

Variant related genes	Relation type
SIPA1	TF binding region
ENSG00000197136	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000172818	Chromatin interaction
ENSG00000255120	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000173327	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1073602	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1074155	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1074156	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10791822	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10896025	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896026	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896028	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10896032	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10896033	0.90[ASN][1000 genomes]
rs10896034	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10896035	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227251	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11227254	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11227281	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs11227299	0.81[CHB][hapmap]
rs11568300	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11601509	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12289836	0.94[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12576766	0.82[ASN][1000 genomes]
rs12802391	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1466462	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236682	0.87[ASN][1000 genomes]
rs2306362	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28464085	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4014195	0.81[CHB][hapmap]
rs4645927	0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs4645933	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs60626743	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61893835	0.87[ASN][1000 genomes]
rs61895665	0.87[ASN][1000 genomes]
rs6591185	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6591187	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6591188	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs7115734	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7120713	0.87[ASN][1000 genomes]
rs7924510	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7930301	0.87[ASN][1000 genomes]
rs7947604	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7952133	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs948494	0.85[MEX][hapmap]
rs9666878	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
4	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
5	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
6	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
8	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
9	nsv468599	chr11:65335705-65427346	ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv555213	chr11:65335705-65427346	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
11	nsv897732	chr11:65335705-65427346	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
12	nsv468600	chr11:65335705-65431360	Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
13	nsv555214	chr11:65335705-65431360	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
14	nsv897733	chr11:65335705-65431360	Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
15	nsv897734	chr11:65335705-65436888	Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
16	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
17	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
18	nsv897746	chr11:65349756-65427346	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
19	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
20	esv1831135	chr11:65387352-65420872	Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	43 gene(s)	inside rSNPs	diseases
21	nsv897748	chr11:65392695-65466911	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
22	nsv897749	chr11:65401748-65420760	Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	39 gene(s)	inside rSNPs	diseases
23	nsv897750	chr11:65401748-65421476	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
24	nsv897751	chr11:65401748-65425167	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
25	nsv897752	chr11:65405300-65421476	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
26	nsv897753	chr11:65405300-65422693	Genic enhancers Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
27	nsv897754	chr11:65405300-65436888	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
28	nsv897755	chr11:65405300-65481166	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
29	nsv897756	chr11:65406393-65425167	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
30	nsv897757	chr11:65406393-65427568	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs746429	PCNXL3	cis	cerebellum	SCAN
rs746429	DRAP1	cis	parietal	SCAN
rs746429	CTSF	cis	cerebellum	SCAN
rs746429	RNASEH2C	cis	parietal	SCAN
rs746429	SIPA1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65406600-65419200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr11:65409200-65419000	Weak transcription	Right Atrium	heart
3	chr11:65410800-65418200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr11:65411200-65419000	Weak transcription	HSMM	muscle
5	chr11:65411400-65418800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr11:65411600-65418600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:65411600-65418800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:65411600-65419000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:65411800-65419200	Strong transcription	Primary T cells from cord blood	blood
10	chr11:65412000-65417600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:65412000-65418800	Weak transcription	Hela-S3	cervix
12	chr11:65412000-65419000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:65412200-65418400	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr11:65412200-65418800	Weak transcription	HepG2	liver
15	chr11:65412400-65417600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:65412400-65418400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:65412600-65419600	Genic enhancers	Fetal Muscle Leg	muscle
18	chr11:65413200-65418000	Weak transcription	Colon Smooth Muscle	Colon
19	chr11:65413200-65418800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:65413400-65418200	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:65413400-65419000	Weak transcription	NHDF-Ad	bronchial
22	chr11:65413600-65418600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:65413600-65419000	Weak transcription	HSMMtube	muscle
24	chr11:65414200-65418000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:65415000-65417800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:65415000-65419000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:65415000-65419000	Weak transcription	Fetal Kidney	kidney
28	chr11:65415200-65418000	Weak transcription	Stomach Mucosa	stomach
29	chr11:65415200-65418800	Weak transcription	Brain Angular Gyrus	brain
30	chr11:65415200-65418800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:65415200-65419200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:65415200-65419200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr11:65415200-65419200	Weak transcription	NH-A	brain
34	chr11:65415200-65419400	Weak transcription	Psoas Muscle	Psoas
35	chr11:65415200-65419400	Weak transcription	Small Intestine	intestine
36	chr11:65415200-65419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:65415400-65417600	Weak transcription	NHEK	skin
38	chr11:65415400-65417800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:65415400-65418200	Strong transcription	Fetal Stomach	stomach
40	chr11:65415400-65418200	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr11:65415400-65418800	Strong transcription	Primary hematopoietic stem cells	blood
42	chr11:65415400-65419000	Weak transcription	Brain Substantia Nigra	brain
43	chr11:65415400-65419000	Weak transcription	A549	lung
44	chr11:65415400-65419200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:65415400-65419200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:65415400-65419200	Weak transcription	Fetal Heart	heart
47	chr11:65415400-65419400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:65415400-65419800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr11:65415600-65418000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr11:65415600-65419200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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