Variant report

Variant	rs3732852
Chromosome Location	chr3:134076154-134076155
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:134075099-134077753	Hela-S3	cervix:	n/a	n/a
2	TEAD4	chr3:134075856-134077787	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr3:134075964-134077712	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:134076061-134077392	HepG2	liver:	n/a	n/a
5	GATA3	chr3:134076151-134077491	SK-N-SH	brain:	n/a	n/a
6	EP300	chr3:134075913-134077492	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr3:134075139-134077732	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr3:134075304-134077814	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr3:134076090-134076591	A549	lung:	n/a	n/a
10	POLR2A	chr3:134075793-134076253	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr3:134076100-134077122	ProgFib	skin:	n/a	n/a
12	POLR2A	chr3:134075038-134079875	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr3:134075907-134077716	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:134074939-134079826	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr3:134075852-134076309	HUVEC	blood vessel:	n/a	n/a
16	PBX3	chr3:134075932-134077653	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr3:134075808-134077598	U87	brain:	n/a	n/a
18	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
19	POLR2A	chr3:134075092-134079606	A549	lung:	n/a	n/a
20	POLR2A	chr3:134075827-134076245	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:134075106-134076303	HUVEC	blood vessel:	n/a	n/a
22	MAZ	chr3:134075111-134077713	IMR90	lung:	n/a	n/a
23	POLR2A	chr3:134075129-134076368	HUVEC	blood vessel:	n/a	n/a
24	TEAD4	chr3:134076106-134077377	SK-N-SH	brain:	n/a	n/a
25	GATA3	chr3:134076073-134077287	MCF-7	breast:	n/a	n/a
26	USF2	chr3:134075061-134077221	Hela-S3	cervix:	n/a	n/a
27	SIN3AK20	chr3:134075943-134077495	MCF-7	breast:	n/a	n/a
28	POLR2A	chr3:134075008-134079572	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:134071303-134093679	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:134075683-134078854	U87	brain:	n/a	n/a
32	EP300	chr3:134075816-134077866	ECC-1	luminal epithelium:	n/a	n/a
33	PBX3	chr3:134076008-134077386	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr3:134074967-134094367	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr3:134075815-134077429	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr3:134074945-134079788	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr3:134076153-134076365	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr3:134069355-134094620	IMR90	lung:	n/a	n/a
39	POLR2A	chr3:134076045-134076407	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:134075053-134079865	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:134074631..134077411-chr3:134204905..134207486,2	MCF-7	breast:
2	chr3:134072948..134076764-chr3:134201781..134206077,4	MCF-7	breast:
3	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
4	chr3:134069007..134072370-chr3:134075638..134078854,3	K562	blood:
5	chr3:133966207..133969204-chr3:134075829..134077344,2	MCF-7	breast:

No data

Variant related genes	Relation type
RPL39P5	TF binding region
ENSG00000214289	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000240006	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10755085	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs10755086	0.84[ASN][1000 genomes]
rs1111516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11708815	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11719057	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12495847	0.80[ASN][1000 genomes]
rs12496438	0.84[ASN][1000 genomes]
rs13075185	0.95[ASN][1000 genomes]
rs13322269	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs1353776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353777	0.80[ASN][1000 genomes]
rs1353778	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1466827	0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1498731	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1603824	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1863910	0.80[ASN][1000 genomes]
rs2133307	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303635	0.88[CHB][hapmap]
rs2400278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2400279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2400280	0.88[ASN][1000 genomes]
rs34341902	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35951257	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755762	0.84[ASN][1000 genomes]
rs3773820	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3821705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264700	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4974485	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974486	1.00[JPT][hapmap]
rs4974489	0.90[ASN][1000 genomes]
rs4974491	0.90[ASN][1000 genomes]
rs4974494	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974495	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974496	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974497	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439478	0.86[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786148	0.90[ASN][1000 genomes]
rs7613066	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9450	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817900	0.90[ASN][1000 genomes]
rs9853621	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3732852	RP11-375I20.6	cis	Artery Aorta	GTEx
rs3732852	RP11-375I20.6	cis	Esophagus Muscularis	GTEx
rs3732852	RP11-375I20.6	cis	Heart Left Ventricle	GTEx
rs3732852	RP11-375I20.6	cis	Artery Tibial	GTEx
rs3732852	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs3732852	TMEM22	cis	parietal	SCAN
rs3732852	RP11-375I20.6	cis	Thyroid	GTEx
rs3732852	FOXL2	cis	parietal	SCAN
rs3732852	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs3732852	RP11-375I20.6	cis	lung	GTEx
rs3732852	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134066600-134076200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:134067600-134076200	Strong transcription	Brain Germinal Matrix	brain
3	chr3:134069200-134090000	Genic enhancers	Fetal Muscle Trunk	muscle
4	chr3:134069400-134089800	Genic enhancers	Fetal Muscle Leg	muscle
5	chr3:134070000-134082400	Genic enhancers	Right Ventricle	heart
6	chr3:134070400-134088200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:134071000-134082600	Genic enhancers	NHLF	lung
8	chr3:134071000-134088800	Enhancers	Right Atrium	heart
9	chr3:134071200-134082400	Genic enhancers	Brain Substantia Nigra	brain
10	chr3:134071400-134079000	Genic enhancers	Fetal Intestine Large	intestine
11	chr3:134071600-134076400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:134071600-134082200	Weak transcription	Primary T cells from cord blood	blood
13	chr3:134071600-134082800	Genic enhancers	Placenta	Placenta
14	chr3:134072000-134079000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:134072000-134082800	Genic enhancers	Lung	lung
16	chr3:134072200-134076600	Weak transcription	Fetal Thymus	thymus
17	chr3:134072200-134082400	Genic enhancers	Brain Hippocampus Middle	brain
18	chr3:134072200-134090200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:134072400-134076600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:134072400-134077200	Genic enhancers	Osteobl	bone
21	chr3:134072400-134091200	Genic enhancers	Spleen	Spleen
22	chr3:134072600-134080200	Weak transcription	Small Intestine	intestine
23	chr3:134072600-134082000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:134072600-134082200	Genic enhancers	Adipose Nuclei	Adipose
25	chr3:134072800-134077000	Genic enhancers	NHEK	skin
26	chr3:134072800-134081000	Genic enhancers	Placenta Amnion	Placenta Amnion
27	chr3:134072800-134082400	Genic enhancers	Brain Cingulate Gyrus	brain
28	chr3:134072800-134082600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:134072800-134090600	Genic enhancers	Left Ventricle	heart
30	chr3:134073000-134076200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:134073000-134076200	Genic enhancers	NHDF-Ad	bronchial
32	chr3:134073000-134076600	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr3:134073000-134077600	Transcr. at gene 5' and 3'	A549	lung
34	chr3:134073000-134078400	Genic enhancers	Fetal Kidney	kidney
35	chr3:134073000-134080400	Genic enhancers	Ovary	ovary
36	chr3:134073000-134082200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:134073000-134089400	Genic enhancers	HMEC	breast
38	chr3:134073200-134076200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:134073200-134076200	Strong transcription	HUVEC	blood vessel
40	chr3:134073200-134076400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:134073200-134076600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:134073200-134077200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:134073200-134078200	Genic enhancers	Fetal Lung	lung
44	chr3:134073200-134079400	Genic enhancers	Esophagus	oesophagus
45	chr3:134073200-134082000	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr3:134073200-134082200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:134073400-134082200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:134073400-134091400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:134073800-134076200	Strong transcription	Colonic Mucosa	Colon
50	chr3:134073800-134082400	Strong transcription	Sigmoid Colon	Sigmoid Colon

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