Variant report

Variant	rs1403631
Chromosome Location	chr3:119358319-119358320
allele	A/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	IKZF1	chr3:119356654-119358681	GM12878	blood:	n/a	n/a
2	NFATC1	chr3:119356456-119358781	GM12878	blood:	n/a	n/a
3	GATA3	chr3:119356390-119359464	SK-N-SH	brain:	n/a	chr3:119357125-119357135 chr3:119357061-119357071
4	RELA	chr3:119356866-119358720	GM12878	blood:	n/a	n/a
5	NFIC	chr3:119356328-119359285	GM12878	blood:	n/a	n/a
6	EP300	chr3:119358318-119359242	SK-N-SH	brain:	n/a	chr3:119358549-119358558
7	GATA3	chr3:119357621-119359298	SH-SY5Y	brain:	n/a	n/a
8	EP300	chr3:119355708-119359660	SK-N-SH	brain:	n/a	chr3:119358021-119358035 chr3:119358549-119358558 chr3:119357930-119357938 chr3:119356957-119356971 chr3:119356958-119356972
9	STAT5A	chr3:119356586-119358828	GM12878	blood:	n/a	chr3:119358550-119358559 chr3:119358549-119358558
10	TBL1XR1	chr3:119357509-119358596	GM12878	blood:	n/a	n/a
11	BHLHE40	chr3:119356827-119358449	GM12878	blood:	n/a	n/a
12	ZNF384	chr3:119356550-119358661	GM12878	blood:	n/a	n/a
13	RELA	chr3:119356737-119358479	GM18951	blood:	n/a	n/a
14	MEF2A	chr3:119357554-119358710	GM12878	blood:	n/a	chr3:119358069-119358083
15	WRNIP1	chr3:119357535-119358487	GM12878	blood:	n/a	n/a
16	STAT5A	chr3:119357418-119358767	GM12878	blood:	n/a	chr3:119358550-119358559 chr3:119358549-119358558
17	TCF12	chr3:119356402-119359447	SK-N-SH	brain:	n/a	chr3:119357774-119357782
18	MYC	chr3:119357690-119358334	K562	blood:	n/a	chr3:119357864-119357873
19	RELA	chr3:119356797-119358637	GM18505	blood:	n/a	n/a
20	RCOR1	chr3:119357563-119358468	GM12878	blood:	n/a	n/a
21	CREB1	chr3:119356463-119358897	GM12878	blood:	n/a	n/a
22	RELA	chr3:119356983-119358425	GM19099	blood:	n/a	n/a
23	CHD2	chr3:119356906-119358581	GM12878	blood:	n/a	n/a
24	RUNX3	chr3:119358208-119358769	GM12878	blood:	n/a	n/a
25	CUX1	chr3:119357482-119358327	GM12878	blood:	n/a	n/a
26	NFATC1	chr3:119357504-119358900	GM12878	blood:	n/a	n/a
27	EBF1	chr3:119356905-119358599	GM12878	blood:	n/a	n/a
28	MXI1	chr3:119356499-119359364	SK-N-SH	brain:	n/a	n/a
29	MTA3	chr3:119356439-119358832	GM12878	blood:	n/a	n/a
30	GATA1	chr3:119357486-119358393	K562	blood:	n/a	n/a
31	IRF4	chr3:119358260-119358828	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:119356373-119358587	GM12878	blood:	n/a	n/a
33	PML	chr3:119356256-119359119	GM12878	blood:	n/a	n/a
34	MAX	chr3:119357017-119358384	GM12878	blood:	n/a	chr3:119357864-119357873
35	RELA	chr3:119356654-119358651	GM12891	blood:	n/a	n/a
36	EP300	chr3:119357640-119358711	GM12878	blood:	n/a	chr3:119358021-119358035 chr3:119358549-119358558 chr3:119357930-119357938
37	SMC3	chr3:119356836-119358557	GM12878	blood:	n/a	chr3:119357131-119357139
38	RELA	chr3:119356875-119358588	GM10847	blood:	n/a	n/a
39	JUND	chr3:119358312-119359237	SK-N-SH	brain:	n/a	chr3:119358550-119358558 chr3:119358549-119358558 chr3:119358575-119358587 chr3:119358551-119358558
40	RUNX3	chr3:119356354-119358964	GM12878	blood:	n/a	n/a
41	JUND	chr3:119356288-119359356	SK-N-SH	brain:	n/a	chr3:119358550-119358558 chr3:119358549-119358558 chr3:119358575-119358587 chr3:119358551-119358558
42	FOSL2	chr3:119358319-119358857	SK-N-SH	brain:	n/a	chr3:119358550-119358558 chr3:119358549-119358558 chr3:119358575-119358587 chr3:119358551-119358558
43	GATA3	chr3:119356512-119359281	SK-N-SH	brain:	n/a	chr3:119357125-119357135 chr3:119357061-119357071
44	NFIC	chr3:119356663-119358976	GM12878	blood:	n/a	n/a
45	CEBPB	chr3:119356654-119358982	GM12878	blood:	n/a	chr3:119357855-119357866 chr3:119357854-119357867
46	EP300	chr3:119356652-119358660	GM12878	blood:	n/a	chr3:119358021-119358035 chr3:119358549-119358558 chr3:119357930-119357938 chr3:119356957-119356971 chr3:119356958-119356972
47	BATF	chr3:119358245-119358943	GM12878	blood:	n/a	chr3:119358624-119358635 chr3:119358546-119358557
48	GATA2	chr3:119357518-119359232	SH-SY5Y	brain:	n/a	n/a
49	CHD1	chr3:119356809-119358320	GM12878	blood:	n/a	n/a
50	ATF2	chr3:119357395-119358814	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119356916..119358623-chr3:119366628..119369264,2	K562	blood:

Variant related genes	Relation type
ENSG00000242052	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11914676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923223	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12487499	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488460	0.94[ASN][1000 genomes]
rs12490779	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12492456	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525836	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16830115	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830291	0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs17203235	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1797827	0.97[ASN][1000 genomes]
rs1872432	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1985121	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280578	0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2670292	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688629	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688630	0.97[ASN][1000 genomes]
rs2688631	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688634	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692616	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698283	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34097211	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34593263	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34787881	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35043554	0.94[ASN][1000 genomes]
rs35256565	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234662	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629367	0.87[ASN][1000 genomes]
rs4687869	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688024	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484809	0.85[JPT][hapmap]
rs524043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571352	0.85[JPT][hapmap]
rs572119	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs575833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579196	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6766563	0.89[CHB][hapmap]
rs67683909	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789941	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790938	0.86[ASN][1000 genomes]
rs6792417	0.87[ASN][1000 genomes]
rs6794579	0.88[JPT][hapmap]
rs6803814	0.89[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs68150601	0.87[ASN][1000 genomes]
rs71325388	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71325389	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613825	0.94[ASN][1000 genomes]
rs7626940	0.89[CHB][hapmap]
rs8422	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876919	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic 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	16 gene(s)	inside rSNPs	diseases
5	esv1796433	chr3:119350324-119360506	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1804126	chr3:119351398-119360506	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv527724	chr3:119353844-119361415	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1403631	COX17	Cis_1M	lymphoblastoid	RTeQTL
rs1403631	COX17	cis	lymphoblastoid	seeQTL
rs1403631	ILDR1	cis	cerebellum	SCAN
rs1403631	POPDC2	cis	lymphoblastoid	seeQTL
rs1403631	POPDC2	cis	multi-tissue	Pritchard

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119341400-119364600	Weak transcription	Liver	Liver
2	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
4	chr3:119352600-119367000	Weak transcription	Ovary	ovary
5	chr3:119353800-119359000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr3:119354000-119358600	Enhancers	Left Ventricle	heart
7	chr3:119354000-119358800	Enhancers	Placenta	Placenta
8	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:119354400-119358400	Enhancers	Adipose Nuclei	Adipose
10	chr3:119354400-119358400	Enhancers	Right Atrium	heart
11	chr3:119354400-119358800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:119354600-119358400	Enhancers	HUVEC	blood vessel
13	chr3:119354800-119358400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:119354800-119358400	Enhancers	HSMM	muscle
15	chr3:119354800-119358600	Enhancers	Small Intestine	intestine
16	chr3:119354800-119358600	Enhancers	HMEC	breast
17	chr3:119354800-119360400	Weak transcription	Lung	lung
18	chr3:119355000-119358400	Enhancers	K562	blood
19	chr3:119355400-119358600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr3:119355400-119361000	Weak transcription	Pancreas	Pancrea
21	chr3:119356000-119358600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:119356200-119360200	Weak transcription	Primary T cells from cord blood	blood
23	chr3:119356200-119360800	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:119356400-119358400	Enhancers	NHEK	skin
26	chr3:119356400-119358600	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:119356400-119358600	Enhancers	Fetal Thymus	thymus
28	chr3:119356600-119358400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:119356600-119358400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr3:119356600-119358400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:119356600-119358600	Enhancers	Dnd41	blood
32	chr3:119356800-119360800	Weak transcription	Aorta	Aorta
33	chr3:119356800-119361400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:119356800-119364800	Weak transcription	Stomach Mucosa	stomach
35	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
37	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:119357000-119358400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr3:119357000-119358600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:119357200-119358400	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:119357200-119358400	Enhancers	Osteobl	bone
42	chr3:119357200-119359200	Enhancers	NHDF-Ad	bronchial
43	chr3:119357200-119361800	Weak transcription	A549	lung
44	chr3:119357200-119383800	Weak transcription	Primary B cells from cord blood	blood
45	chr3:119357400-119358600	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:119357600-119358400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:119357600-119358400	Enhancers	Esophagus	oesophagus
48	chr3:119357600-119358400	Flanking Active TSS	GM12878-XiMat	blood
49	chr3:119357800-119358600	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr3:119357800-119358600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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