Variant report

Variant	rs2400278
Chromosome Location	chr3:134073100-134073101
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	POLR2A	chr3:134072666-134073888	HUVEC	blood vessel:	n/a	n/a
2	MAX	chr3:134072373-134074291	A549	lung:	n/a	chr3:134073303-134073313 chr3:134073289-134073299 chr3:134073568-134073577 chr3:134073263-134073273 chr3:134073317-134073327 chr3:134073367-134073376
3	POLR2A	chr3:134072937-134074174	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:134071214-134074714	HUVEC	blood vessel:	n/a	n/a
5	USF2	chr3:134072957-134074701	Hela-S3	cervix:	n/a	n/a
6	MAX	chr3:134073068-134073462	A549	lung:	n/a	chr3:134073303-134073313 chr3:134073289-134073299 chr3:134073263-134073273 chr3:134073317-134073327 chr3:134073367-134073376
7	GATA3	chr3:134072754-134073293	T-47D	breast:	n/a	n/a
8	TEAD4	chr3:134072298-134073856	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr3:134071448-134074783	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:134072615-134073860	A549	lung:	n/a	n/a
11	POLR2A	chr3:134072936-134073697	H1-neurons	neurons:	n/a	n/a
12	BCL3	chr3:134072198-134073949	A549	lung:	n/a	n/a
13	PBX3	chr3:134072595-134073480	SK-N-SH	brain:	n/a	chr3:134073165-134073174
14	MAX	chr3:134071949-134074597	A549	lung:	n/a	chr3:134073303-134073313 chr3:134073289-134073299 chr3:134073568-134073577 chr3:134073263-134073273 chr3:134073317-134073327 chr3:134073367-134073376
15	POLR2A	chr3:134073099-134073330	A549	lung:	n/a	n/a
16	MAX	chr3:134072628-134074482	ECC-1	luminal epithelium:	n/a	chr3:134073303-134073313 chr3:134073289-134073299 chr3:134073568-134073577 chr3:134073263-134073273 chr3:134073317-134073327 chr3:134073367-134073376
17	POLR2A	chr3:134072616-134073378	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr3:134071878-134074839	HUVEC	blood vessel:	n/a	n/a
19	NFIC	chr3:134072510-134073339	ECC-1	luminal epithelium:	n/a	n/a
20	SIN3AK20	chr3:134072626-134073703	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr3:134072044-134074473	ProgFib	skin:	n/a	n/a
22	POLR2A	chr3:134071621-134074470	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr3:134071059-134074572	ECC-1	luminal epithelium:	n/a	n/a
24	BCL3	chr3:134072238-134073667	A549	lung:	n/a	n/a
25	PBX3	chr3:134072592-134073677	SK-N-SH	brain:	n/a	chr3:134073165-134073174
26	POLR2A	chr3:134072939-134073757	U87	brain:	n/a	n/a
27	POLR2A	chr3:134072477-134074140	MCF-7	breast:	n/a	n/a
28	POLR2A	chr3:134071177-134074761	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUND	chr3:134072124-134073646	SK-N-SH	brain:	n/a	n/a
30	TCF12	chr3:134071925-134074047	ECC-1	luminal epithelium:	n/a	chr3:134072159-134072169
31	POLR2A	chr3:134072902-134074190	U87	brain:	n/a	n/a
32	FOXA1	chr3:134072918-134073389	T-47D	breast:	n/a	n/a
33	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
34	MAX	chr3:134072444-134073800	MCF-7	breast:	n/a	chr3:134073303-134073313 chr3:134073289-134073299 chr3:134073568-134073577 chr3:134073263-134073273 chr3:134073317-134073327 chr3:134073367-134073376
35	POLR2A	chr3:134072648-134074207	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:134071949-134074646	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr3:134073097-134073798	HepG2	liver:	n/a	n/a
38	PBX3	chr3:134072635-134073627	A549	lung:	n/a	chr3:134073165-134073174
39	MAX	chr3:134072798-134073856	ECC-1	luminal epithelium:	n/a	chr3:134073303-134073313 chr3:134073289-134073299 chr3:134073568-134073577 chr3:134073263-134073273 chr3:134073317-134073327 chr3:134073367-134073376
40	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
41	TCF12	chr3:134072350-134073678	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr3:134071051-134074609	ECC-1	luminal epithelium:	n/a	n/a
43	RAD21	chr3:134070902-134074481	IMR90	lung:	n/a	chr3:134071273-134071282 chr3:134073072-134073086 chr3:134071271-134071281 chr3:134071467-134071480 chr3:134073738-134073752 chr3:134071329-134071338
44	MAX	chr3:134073008-134073353	Hela-S3	cervix:	n/a	chr3:134073303-134073313 chr3:134073289-134073299 chr3:134073263-134073273 chr3:134073317-134073327
45	POLR2A	chr3:134071303-134093679	HepG2	liver:	n/a	n/a
46	E2F6	chr3:134072651-134073477	A549	lung:	n/a	n/a
47	PBX3	chr3:134072651-134073277	A549	lung:	n/a	chr3:134073165-134073174
48	POLR2A	chr3:134072689-134074108	A549	lung:	n/a	n/a
49	POLR2A	chr3:134071863-134074701	U87	brain:	n/a	n/a
50	POLR2A	chr3:134071236-134074903	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:134072948..134076764-chr3:134201781..134206077,4	MCF-7	breast:
2	chr3:134071025..134073147-chr3:134182309..134183857,2	MCF-7	breast:
3	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
4	chr3:134052518..134054585-chr3:134071720..134074558,2	K562	blood:
5	chr3:134071281..134073530-chr3:134186337..134189108,2	MCF-7	breast:

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

Extended variants
information (count: 40 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10755085	1.00[CHB][hapmap];0.86[CHD][hapmap]
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];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708815	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11719057	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13075185	0.90[ASN][1000 genomes]
rs13322269	0.89[CHB][hapmap]
rs1353776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1353778	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs1466827	0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1498731	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603824	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133307	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303635	0.88[CHB][hapmap]
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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400280	0.93[ASN][1000 genomes]
rs34341902	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951257	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732852	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]
rs3773820	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3821705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264700	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974485	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974486	1.00[JPT][hapmap]
rs4974487	0.84[ASN][1000 genomes]
rs4974489	0.95[ASN][1000 genomes]
rs4974491	0.95[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];0.93[EUR][1000 genomes];1.00[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];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974497	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974498	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439478	0.86[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786148	0.95[ASN][1000 genomes]
rs7613066	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817900	0.95[ASN][1000 genomes]
rs9853621	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[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
rs2400278	FOXL2	cis	parietal	SCAN
rs2400278	RP11-375I20.6	cis	Heart Left Ventricle	GTEx
rs2400278	RP11-375I20.6	cis	Thyroid	GTEx
rs2400278	TMEM22	cis	parietal	SCAN
rs2400278	RP11-375I20.6	cis	Artery Aorta	GTEx
rs2400278	RP11-375I20.6	cis	Artery Tibial	GTEx
rs2400278	RP11-375I20.6	cis	Esophagus Muscularis	GTEx
rs2400278	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs2400278	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs2400278	RP11-375I20.6	cis	lung	GTEx
rs2400278	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:98 , 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	chr3:134067000-134073400	Enhancers	Pancreas	Pancrea
3	chr3:134067400-134073200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:134067400-134073200	Enhancers	Esophagus	oesophagus
5	chr3:134067600-134073200	Weak transcription	Brain Angular Gyrus	brain
6	chr3:134067600-134076200	Strong transcription	Brain Germinal Matrix	brain
7	chr3:134067800-134073200	Weak transcription	NH-A	brain
8	chr3:134068400-134073200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:134068400-134074200	Genic enhancers	Fetal Intestine Small	intestine
10	chr3:134068400-134076000	Strong transcription	Fetal Stomach	stomach
11	chr3:134068800-134073200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:134069000-134074000	Strong transcription	Fetal Brain Female	brain
13	chr3:134069000-134074600	Enhancers	Psoas Muscle	Psoas
14	chr3:134069000-134076000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:134069200-134074600	Enhancers	Stomach Mucosa	stomach
16	chr3:134069200-134090000	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr3:134069400-134073400	Enhancers	Liver	Liver
18	chr3:134069400-134089800	Genic enhancers	Fetal Muscle Leg	muscle
19	chr3:134069600-134073200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:134069600-134073400	Enhancers	HepG2	liver
21	chr3:134070000-134082400	Genic enhancers	Right Ventricle	heart
22	chr3:134070400-134073600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:134070400-134075000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:134070400-134075000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:134070400-134088200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:134070600-134073200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:134070600-134073200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:134071000-134075800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:134071000-134082600	Genic enhancers	NHLF	lung
30	chr3:134071000-134088800	Enhancers	Right Atrium	heart
31	chr3:134071200-134073200	Enhancers	Fetal Heart	heart
32	chr3:134071200-134073200	Weak transcription	HUVEC	blood vessel
33	chr3:134071200-134082400	Genic enhancers	Brain Substantia Nigra	brain
34	chr3:134071400-134075200	Strong transcription	Aorta	Aorta
35	chr3:134071400-134079000	Genic enhancers	Fetal Intestine Large	intestine
36	chr3:134071600-134073200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:134071600-134073200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:134071600-134076000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:134071600-134076400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:134071600-134082200	Weak transcription	Primary T cells from cord blood	blood
41	chr3:134071600-134082800	Genic enhancers	Placenta	Placenta
42	chr3:134071800-134073200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:134071800-134074000	Weak transcription	Hela-S3	cervix
44	chr3:134071800-134075400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:134072000-134073800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr3:134072000-134079000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:134072000-134082800	Genic enhancers	Lung	lung
48	chr3:134072200-134073200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:134072200-134073200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:134072200-134073200	Genic enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links