Variant report

Variant	rs10501321
Chromosome Location	chr11:47294626-47294627
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	REST	chr11:47294159-47294799	K562	blood:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
2	REST	chr11:47294123-47294747	PANC-1	pancreas:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
3	REST	chr11:47294294-47294678	PFSK-1	brain:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
4	REST	chr11:47294183-47294653	H1-hESC	embryonic stem cell:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
5	REST	chr11:47294219-47294879	PFSK-1	brain:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
6	REST	chr11:47293798-47294917	ECC-1	luminal epithelium:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
7	REST	chr11:47294141-47294787	A549	lung:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
8	REST	chr11:47294259-47294628	A549	lung:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
9	REST	chr11:47293917-47294874	SK-N-SH	brain:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
10	REST	chr11:47294204-47294711	HL-60	blood:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
11	REST	chr11:47294228-47294679	HepG2	liver:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
12	REST	chr11:47294077-47294802	MCF-7	breast:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
13	CEBPB	chr11:47294348-47294679	Hela-S3	cervix:	n/a	chr11:47294519-47294530 chr11:47294519-47294530
14	REST	chr11:47294260-47294683	HCT-116	colon:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
15	USF2	chr11:47294397-47294651	Hela-S3	cervix:	n/a	chr11:47294554-47294565
16	REST	chr11:47293898-47294947	PFSK-1	brain:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
17	REST	chr11:47294246-47294796	Hela-S3	cervix:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
18	CEBPB	chr11:47294364-47294664	IMR90	lung:	n/a	chr11:47294519-47294530 chr11:47294519-47294530
19	REST	chr11:47294240-47294628	H1-hESC	embryonic stem cell:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
20	REST	chr11:47293894-47294905	GM12878	blood:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
21	REST	chr11:47294196-47294652	HCT-116	colon:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
22	REST	chr11:47294162-47294736	PANC-1	pancreas:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
23	REST	chr11:47293955-47294880	ECC-1	luminal epithelium:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
24	REST	chr11:47294268-47294647	SK-N-SH	brain:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
25	REST	chr11:47294207-47294821	MCF-7	breast:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
26	REST	chr11:47294255-47294628	PANC-1	pancreas:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
27	REST	chr11:47293506-47294886	HL-60	blood:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
28	REST	chr11:47293917-47294740	Hela-S3	cervix:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
29	TEAD4	chr11:47294269-47294727	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47285533..47287740-chr11:47294426..47296494,3	K562	blood:
2	chr11:47289567..47294786-chr11:47310778..47315538,7	MCF-7	breast:
3	chr11:47263865..47272320-chr11:47288426..47294726,14	MCF-7	breast:
4	chr11:47293111..47295014-chr11:47788351..47790710,2	MCF-7	breast:

Variant related genes	Relation type
MADD	TF binding region
ENSG00000256746	TF binding region
ENSG00000110514	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000109920	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1052373	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1055510	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742799	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742801	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10769252	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10838681	0.86[MEX][hapmap];0.81[TSI][hapmap]
rs10838684	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10838687	0.83[CHB][hapmap]
rs10838690	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10838691	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838692	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838693	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039156	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11039166	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039167	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12575456	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1375688	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1449627	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013867	0.98[GIH][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2167079	0.94[ASW][hapmap];0.98[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2269434	0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs2279239	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2291119	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2301216	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs326214	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326217	0.83[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs326222	0.88[ASW][hapmap];0.98[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs35879051	0.89[EUR][1000 genomes]
rs3758669	0.85[EUR][1000 genomes]
rs3758672	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3758673	0.98[GIH][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3781621	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3781622	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816725	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3847502	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4752822	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4752824	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4752825	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752980	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59663860	0.89[EUR][1000 genomes]
rs61896050	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485746	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7109147	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7109203	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7120118	0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7120957	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7124955	1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7127907	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7129661	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7395581	0.98[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs753993	0.83[CHB][hapmap]
rs7940809	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs830085	0.98[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs901746	0.94[ASW][hapmap];0.98[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10501321	NR1H3	cis	lymphoblastoid	seeQTL
rs10501321	ACP2	cis	Thyroid	GTEx
rs10501321	DDB2	cis	lymphoblastoid	seeQTL
rs10501321	MADD	cis	cerebellum	SCAN
rs10501321	MTCH2	cis	cerebellum	SCAN
rs10501321	ACP2	cis	lymphoblastoid	seeQTL
rs10501321	ACP2	cis	multi-tissue	Pritchard
rs10501321	NR1H3	cis	parietal	SCAN
rs10501321	ATG13	cis	cerebellum	SCAN
rs10501321	PACSIN3	cis	Esophagus Mucosa	GTEx
rs10501321	MADD	cis	parietal	SCAN
rs10501321	DGKZ	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47292600-47294800	Enhancers	Psoas Muscle	Psoas
2	chr11:47292600-47294800	Enhancers	Stomach Mucosa	stomach
3	chr11:47292600-47295800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:47292600-47296000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:47292600-47296000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:47292600-47296000	Weak transcription	Ovary	ovary
7	chr11:47292600-47296200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:47292800-47294800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:47292800-47294800	Flanking Active TSS	GM12878-XiMat	blood
10	chr11:47292800-47295200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr11:47292800-47296200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:47292800-47296200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:47293000-47294800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:47293000-47294800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr11:47293000-47294800	Enhancers	Adipose Nuclei	Adipose
16	chr11:47293000-47294800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr11:47293000-47294800	Enhancers	Fetal Muscle Leg	muscle
18	chr11:47293000-47295200	Enhancers	Primary B cells from peripheral blood	blood
19	chr11:47293000-47295400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:47293000-47295600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:47293000-47295800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:47293000-47296000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:47293000-47296200	Weak transcription	Fetal Kidney	kidney
24	chr11:47293000-47296400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr11:47293000-47296600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:47293000-47296600	Weak transcription	NH-A	brain
27	chr11:47293200-47295000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:47293200-47295200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:47293200-47295200	Weak transcription	Osteobl	bone
30	chr11:47293200-47295400	Weak transcription	Placenta	Placenta
31	chr11:47293200-47295400	Weak transcription	NHLF	lung
32	chr11:47293200-47296000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:47293200-47296000	Weak transcription	Esophagus	oesophagus
34	chr11:47293200-47296200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:47293200-47296200	Weak transcription	HMEC	breast
36	chr11:47293200-47297000	Weak transcription	HUVEC	blood vessel
37	chr11:47293600-47294800	Enhancers	Right Atrium	heart
38	chr11:47293600-47295000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr11:47293600-47296000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:47293600-47296200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:47293600-47296600	Weak transcription	A549	lung
42	chr11:47293600-47296600	Weak transcription	NHDF-Ad	bronchial
43	chr11:47293800-47294800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr11:47293800-47294800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr11:47293800-47294800	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr11:47293800-47294800	Genic enhancers	Hela-S3	cervix
47	chr11:47293800-47295400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:47293800-47295600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:47293800-47296000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:47293800-47296000	Weak transcription	Pancreas	Pancrea

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