Variant report

Variant	rs558114
Chromosome Location	chr11:65632262-65632263
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65631446-65639140	PANC-1	pancreas:	n/a	n/a
2	PBX3	chr11:65630948-65633633	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr11:65630365-65633811	ProgFib	skin:	n/a	n/a
4	POLR2A	chr11:65617092-65633870	K562	blood:	n/a	n/a
5	POLR2A	chr11:65630140-65633694	GM12892	blood:	n/a	n/a
6	POLR2A	chr11:65632225-65632469	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr11:65616755-65639999	U87	brain:	n/a	n/a
8	POLR2A	chr11:65630406-65632402	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:65629110-65633804	K562	blood:	n/a	n/a
10	POLR2A	chr11:65630217-65632301	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr11:65616706-65640269	U87	brain:	n/a	n/a
12	POLR2A	chr11:65630762-65633743	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr11:65631772-65632728	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr11:65631720-65632582	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:65631707-65632385	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr11:65616501-65633874	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:65630574-65632265	GM12892	blood:	n/a	n/a
18	POLR2A	chr11:65631465-65632610	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr11:65631430-65637395	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr11:65631907-65632514	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr11:65630265-65633866	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65632119..65634475-chr11:65750452..65752204,2	MCF-7	breast:
2	chr11:65546347..65549308-chr11:65631911..65633845,2	MCF-7	breast:
3	chr11:65631727..65633927-chr11:65768782..65771616,2	MCF-7	breast:

No data

Variant related genes	Relation type
MUS81	TF binding region
CFL1	TF binding region
ENSG00000175334	Chromatin interaction
ENSG00000254867	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000175827	Chromatin interaction
ENSG00000254470	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10791828	0.81[CEU][hapmap];0.85[AMR][1000 genomes]
rs10896053	0.88[GIH][hapmap]
rs11227311	0.84[GIH][hapmap]
rs1204772	0.88[GIH][hapmap]
rs12575663	0.80[GIH][hapmap]
rs13817	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939212	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538394	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545500	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570387	0.80[GIH][hapmap]
rs601887	0.88[GIH][hapmap]
rs621348	0.88[GIH][hapmap]
rs630303	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630755	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs633800	0.80[GIH][hapmap]
rs633877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652021	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656040	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659824	0.80[GIH][hapmap];0.86[MKK][hapmap]
rs659857	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs665306	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667555	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs668356	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7107912	0.84[GIH][hapmap]
rs7114014	0.92[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap]
rs7114237	0.88[GIH][hapmap]
rs7125986	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7947741	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7947929	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
3	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers 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 target site	178 gene(s)	inside rSNPs	diseases
5	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
7	nsv555215	chr11:65581579-65676516	Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
8	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
9	nsv897763	chr11:65613348-65644027	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	121 gene(s)	inside rSNPs	diseases
10	nsv897764	chr11:65613348-65695222	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
11	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
12	nsv897766	chr11:65624025-65644027	Transcr. at gene 5' and 3' Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs558114	DPP3	cis	lymphoblastoid	seeQTL
rs558114	PACS1	cis	parietal	SCAN
rs558114	SNX32	cis	parietal	SCAN
rs558114	SNX32	cis	Whole Blood	GTEx
rs558114	PLCB3	cis	parietal	SCAN
rs558114	SNORD31	cis	cerebellum	SCAN
rs558114	FIBP	cis	cerebellum	SCAN
rs558114	RAB3IL1	cis	cerebellum	SCAN
rs558114	SNX32	cis	Artery Tibial	GTEx
rs558114	SNX32	cis	cerebellum	SCAN
rs558114	SNX32	cis	Esophagus Muscularis	GTEx
rs558114	EIF1AD	cis	parietal	SCAN
rs558114	SNX32	cis	Thyroid	GTEx
rs558114	FIBP	Cis_1M	lymphoblastoid	RTeQTL
rs558114	CARNS1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65628200-65633600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:65628800-65639600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:65629000-65632600	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr11:65629000-65639600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:65629200-65632800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:65629200-65634600	Strong transcription	Aorta	Aorta
7	chr11:65629400-65632600	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr11:65629400-65633200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:65629400-65634400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr11:65629400-65634400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:65629400-65634800	Strong transcription	Brain Substantia Nigra	brain
12	chr11:65629400-65635200	Strong transcription	Brain Anterior Caudate	brain
13	chr11:65629400-65638600	Weak transcription	Right Atrium	heart
14	chr11:65629600-65633400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:65629600-65633400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:65629600-65633600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:65629600-65633600	Strong transcription	Brain Angular Gyrus	brain
18	chr11:65629600-65633800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:65629600-65634400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:65629600-65634400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr11:65629600-65634600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr11:65629600-65634800	Strong transcription	Primary T cells from cord blood	blood
23	chr11:65629600-65635000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:65629600-65635000	Strong transcription	Esophagus	oesophagus
25	chr11:65629600-65635400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:65629600-65635600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr11:65629600-65635800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr11:65629600-65636000	Strong transcription	Thymus	Thymus
29	chr11:65629600-65637400	Strong transcription	Ovary	ovary
30	chr11:65629600-65637600	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr11:65629600-65638000	Strong transcription	Fetal Lung	lung
32	chr11:65629800-65633000	Genic enhancers	Dnd41	blood
33	chr11:65629800-65633600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr11:65629800-65633600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:65629800-65633600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:65629800-65633600	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr11:65629800-65633800	Strong transcription	Primary B cells from cord blood	blood
38	chr11:65629800-65634400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:65629800-65634400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:65629800-65634800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:65629800-65634800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:65629800-65634800	Strong transcription	Fetal Brain Female	brain
43	chr11:65629800-65635000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:65629800-65635400	Strong transcription	Liver	Liver
45	chr11:65629800-65635400	Strong transcription	NHLF	lung
46	chr11:65629800-65635600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:65629800-65636000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:65630000-65633400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr11:65630000-65633600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr11:65630000-65633800	Strong transcription	Rectal Smooth Muscle	rectum

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