Variant report

Variant	rs1131925
Chromosome Location	chr3:155572129-155572130
allele	A/G
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	chr3:155571829-155572774	HepG2	liver:	n/a	n/a
2	MAZ	chr3:155571782-155572807	GM12878	blood:	n/a	chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572487-155572496 chr3:155572487-155572496
3	POLR2A	chr3:155571851-155573277	PANC-1	pancreas:	n/a	n/a
4	MAX	chr3:155571780-155573145	A549	lung:	n/a	chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572487-155572496 chr3:155572487-155572496 chr3:155572536-155572546
5	MAX	chr3:155571951-155572961	H1-hESC	embryonic stem cell:	n/a	chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572487-155572496 chr3:155572487-155572496 chr3:155572536-155572546
6	SMARCB1	chr3:155571014-155573107	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr3:155571976-155573154	A549	lung:	n/a	chr3:155572287-155572295
8	POLR2A	chr3:155571254-155572973	GM15510	blood:	n/a	n/a
9	USF1	chr3:155571732-155573096	HCT-116	colon:	n/a	chr3:155572041-155572057 chr3:155572487-155572496 chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572485-155572496 chr3:155572486-155572495 chr3:155572488-155572497
10	CHD2	chr3:155571816-155572872	GM12878	blood:	n/a	n/a
11	NFYB	chr3:155572092-155572762	K562	blood:	n/a	chr3:155572284-155572297 chr3:155572284-155572299 chr3:155572286-155572296 chr3:155572284-155572298 chr3:155572284-155572299
12	IRF1	chr3:155571952-155572866	K562	blood:	n/a	n/a
13	TAF1	chr3:155571598-155572741	K562	blood:	n/a	n/a
14	RELA	chr3:155571798-155573084	GM18505	blood:	n/a	n/a
15	YY1	chr3:155572064-155572827	GM12878	blood:	n/a	n/a
16	FOXM1	chr3:155571852-155572754	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:155571438-155572935	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:155571860-155572880	K562	blood:	n/a	n/a
19	SIX5	chr3:155571905-155572865	A549	lung:	n/a	n/a
20	MEF2A	chr3:155571953-155572612	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:155571558-155572792	H1-neurons	neurons:	n/a	n/a
22	CREB1	chr3:155571665-155572956	HepG2	liver:	n/a	n/a
23	REST	chr3:155571813-155572938	A549	lung:	n/a	chr3:155571942-155571956 chr3:155572042-155572055
24	ZC3H11A	chr3:155571999-155572845	K562	blood:	n/a	n/a
25	POLR2A	chr3:155571199-155573067	GM12892	blood:	n/a	n/a
26	STAT3	chr3:155572125-155572579	MCF10A-Er-Src	breast:	n/a	chr3:155572222-155572230
27	EP300	chr3:155571954-155572917	ECC-1	luminal epithelium:	n/a	chr3:155572531-155572539
28	E2F4	chr3:155572115-155573062	MCF10A-Er-Src	breast:	n/a	n/a
29	USF1	chr3:155572101-155572877	SK-N-SH_RA	brain:	n/a	chr3:155572487-155572496 chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572485-155572496 chr3:155572486-155572495 chr3:155572488-155572497
30	POU2F2	chr3:155571964-155572806	GM12891	blood:	n/a	chr3:155572771-155572784
31	USF1	chr3:155572055-155572790	A549	lung:	n/a	chr3:155572487-155572496 chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572485-155572496 chr3:155572486-155572495 chr3:155572488-155572497
32	MAX	chr3:155571832-155572993	ECC-1	luminal epithelium:	n/a	chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572487-155572496 chr3:155572487-155572496 chr3:155572536-155572546
33	MYC	chr3:155571461-155573062	K562	blood:	n/a	chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572487-155572496 chr3:155572487-155572496 chr3:155572536-155572546
34	TAF1	chr3:155571959-155572714	Hela-S3	cervix:	n/a	n/a
35	NFATC1	chr3:155571981-155572662	GM12878	blood:	n/a	n/a
36	MAX	chr3:155572036-155572807	K562	blood:	n/a	chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572487-155572496 chr3:155572487-155572496 chr3:155572536-155572546
37	POLR2A	chr3:155571900-155572844	A549	lung:	n/a	n/a
38	USF1	chr3:155571973-155572915	SK-N-SH	brain:	n/a	chr3:155572041-155572057 chr3:155572487-155572496 chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572485-155572496 chr3:155572486-155572495 chr3:155572488-155572497
39	YY1	chr3:155571956-155572788	SK-N-SH	brain:	n/a	n/a
40	E2F4	chr3:155572061-155572744	K562	blood:	n/a	n/a
41	ELK1	chr3:155572059-155572759	K562	blood:	n/a	n/a
42	CREB1	chr3:155572056-155572836	H1-hESC	embryonic stem cell:	n/a	n/a
43	TAF1	chr3:155571716-155572740	HepG2	liver:	n/a	n/a
44	MAZ	chr3:155571693-155573048	K562	blood:	n/a	chr3:155572487-155572496 chr3:155572485-155572498 chr3:155572487-155572496 chr3:155572487-155572496
45	SIN3AK20	chr3:155572086-155572494	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr3:155571908-155572794	HUVEC	blood vessel:	n/a	n/a
47	CTCF	chr3:155572060-155572210	HCFaa	heart:	n/a	n/a
48	GATA1	chr3:155571623-155573116	PBDE	blood:	n/a	n/a
49	ATF3	chr3:155572129-155572982	K562	blood:	n/a	chr3:155572476-155572496 chr3:155572487-155572496
50	IRF4	chr3:155572037-155572812	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:155462054..155464221-chr3:155571081..155573574,2	MCF-7	breast:
2	chr3:155570444..155573449-chr3:155586982..155591161,10	MCF-7	breast:
3	chr3:155521670..155525457-chr3:155569550..155572694,3	MCF-7	breast:
4	chr3:155460891..155464537-chr3:155570941..155574143,3	MCF-7	breast:
5	chr3:155571664..155572210-chr6:119255210..119256056,2	Hela-S3	cervix:
6	chr3:155568718..155574348-chr3:155586235..155593210,15	K562	blood:
7	chr3:155569630..155574596-chr3:155585012..155589734,13	MCF-7	breast:
8	chr3:155522731..155527439-chr3:155568712..155573851,7	MCF-7	breast:
9	chr22:22005850..22008007-chr3:155571064..155572872,2	K562	blood:

Variant related genes	Relation type
SLC33A1	TF binding region
ENSG00000100023	Chromatin interaction
ENSG00000111877	Chromatin interaction
ENSG00000174928	Chromatin interaction
ENSG00000207751	Chromatin interaction
ENSG00000253194	Chromatin interaction
ENSG00000163655	Chromatin interaction
ENSG00000114805	Chromatin interaction
ENSG00000212102	Chromatin interaction
ENSG00000214919	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10804773	0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10804774	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10936020	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11714133	0.85[ASN][1000 genomes]
rs13059611	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2063903	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2200707	0.81[JPT][hapmap]
rs35321137	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358703	0.87[MEX][hapmap]
rs3772115	0.83[ASN][1000 genomes]
rs3772116	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3821365	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4680219	0.86[ASN][1000 genomes]
rs4680223	0.80[ASN][1000 genomes]
rs55662848	0.83[ASN][1000 genomes]
rs6441028	0.96[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66509404	0.89[ASN][1000 genomes]
rs6799267	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6804740	0.84[JPT][hapmap]
rs6809229	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7619976	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7633168	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7643630	0.99[ASN][1000 genomes]
rs7651038	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7652005	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753744	chr3:155487298-155707298	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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 target site	31 gene(s)	inside rSNPs	diseases
3	nsv877681	chr3:155535670-155654017	Weak transcription Enhancers Flanking Active TSS 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 target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1131925	SMC4	cis	cerebellum	SCAN
rs1131925	PLCH1	cis	parietal	SCAN
rs1131925	SLC33A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155568200-155573200	Active TSS	Pancreas	Pancrea
2	chr3:155568600-155573200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:155569400-155572200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:155569400-155572600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:155569400-155573000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:155569400-155573200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:155569400-155573200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:155569400-155573200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:155569600-155572800	Active TSS	Gastric	stomach
10	chr3:155569600-155573000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:155569600-155573000	Active TSS	Left Ventricle	heart
12	chr3:155569600-155573200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr3:155569600-155573200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr3:155569600-155573400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:155569800-155572600	Active TSS	K562	blood
16	chr3:155569800-155573200	Active TSS	Aorta	Aorta
17	chr3:155569800-155573200	Active TSS	NHDF-Ad	bronchial
18	chr3:155569800-155573400	Active TSS	GM12878-XiMat	blood
19	chr3:155570000-155573000	Active TSS	Colonic Mucosa	Colon
20	chr3:155570000-155573000	Active TSS	NHLF	lung
21	chr3:155570000-155573200	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr3:155570000-155573200	Active TSS	Fetal Kidney	kidney
23	chr3:155570000-155573200	Active TSS	HSMM	muscle
24	chr3:155570000-155573200	Active TSS	HSMMtube	muscle
25	chr3:155570000-155573400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:155570200-155572200	Bivalent/Poised TSS	HepG2	liver
27	chr3:155570200-155572800	Active TSS	Stomach Mucosa	stomach
28	chr3:155570200-155573000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr3:155570200-155573000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:155570200-155573000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:155570200-155573000	Active TSS	Lung	lung
32	chr3:155570200-155573000	Active TSS	NHEK	skin
33	chr3:155570200-155573400	Active TSS	A549	lung
34	chr3:155570400-155573000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:155570400-155573000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:155570400-155573000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:155570400-155573000	Active TSS	Esophagus	oesophagus
38	chr3:155570400-155573000	Active TSS	Ovary	ovary
39	chr3:155570400-155573200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:155570400-155573200	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr3:155570600-155573000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:155570600-155573000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:155570600-155573000	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr3:155570600-155573000	Active TSS	Small Intestine	intestine
45	chr3:155570600-155573200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr3:155570600-155573200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:155570600-155573400	Active TSS	HMEC	breast
48	chr3:155570800-155572600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr3:155570800-155572600	Active TSS	HUVEC	blood vessel
50	chr3:155570800-155573000	Active TSS	H9 Cell Line	embryonic stem cell

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