Variant report

Variant	rs7610939
Chromosome Location	chr3:160393545-160393546
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	NR2F2	chr3:160393370-160393936	MCF-7	breast:	n/a	n/a
2	GATA3	chr3:160393365-160393964	T-47D	breast:	n/a	n/a
3	FOS	chr3:160393349-160393818	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr3:160393416-160393833	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr3:160393412-160393612	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr3:160393274-160393747	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr3:160393289-160393753	T-47D	breast:	n/a	chr3:160393715-160393725
8	FOXA1	chr3:160393327-160393852	T-47D	breast:	n/a	chr3:160393531-160393546
9	POLR2A	chr3:160393446-160393748	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr3:160393443-160393781	MCF10A-Er-Src	breast:	n/a	n/a
11	GATA3	chr3:160393432-160393996	MCF-7	breast:	n/a	n/a
12	GATA3	chr3:160393437-160393865	T-47D	breast:	n/a	n/a
13	FOXA2	chr3:160393394-160393856	A549	lung:	n/a	n/a
14	FOXA1	chr3:160393407-160393861	T-47D	breast:	n/a	chr3:160393531-160393546
15	POLR2A	chr3:160393325-160393800	PANC-1	pancreas:	n/a	n/a
16	FOXA2	chr3:160393413-160393551	HepG2	liver:	n/a	n/a
17	FOS	chr3:160393415-160393795	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160283415..160285026-chr3:160392303..160394437,2	MCF-7	breast:
2	chr3:160392640..160394500-chr3:160414229..160416051,2	MCF-7	breast:

Variant related genes	Relation type
ARL14	TF binding region
ENSG00000207084	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10936203	0.80[CEU][hapmap]
rs10936207	0.87[ASN][1000 genomes]
rs10936208	0.86[ASN][1000 genomes]
rs10936209	0.87[ASN][1000 genomes]
rs10936210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712392	0.82[EUR][1000 genomes]
rs11713230	0.82[EUR][1000 genomes]
rs11714916	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11927913	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490985	0.82[ASN][1000 genomes]
rs12639488	0.88[CEU][hapmap]
rs13065269	0.82[EUR][1000 genomes]
rs13074231	0.82[EUR][1000 genomes]
rs13095931	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1317085	0.87[ASN][1000 genomes]
rs1403045	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1522285	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236586	0.92[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs1879797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882125	0.84[CEU][hapmap]
rs1980277	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141668	0.81[EUR][1000 genomes]
rs2178451	0.81[EUR][1000 genomes]
rs2178452	0.87[ASN][1000 genomes]
rs2367209	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28544045	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28730907	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34362576	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34949451	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35008770	0.81[EUR][1000 genomes]
rs35308461	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35480231	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35498840	0.84[CEU][hapmap]
rs35664264	0.87[ASN][1000 genomes]
rs35867836	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36118017	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4133253	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679659	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4679660	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4679903	0.81[EUR][1000 genomes]
rs4679904	0.82[EUR][1000 genomes]
rs4679909	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs57718211	0.80[EUR][1000 genomes]
rs62272216	0.87[ASN][1000 genomes]
rs62272217	0.87[ASN][1000 genomes]
rs62272218	0.87[ASN][1000 genomes]
rs62272219	0.81[ASN][1000 genomes]
rs62272220	0.90[ASN][1000 genomes]
rs6763757	0.83[AMR][1000 genomes]
rs6763892	0.83[AMR][1000 genomes]
rs6773389	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6774379	0.87[ASN][1000 genomes]
rs6774566	0.87[ASN][1000 genomes]
rs6776873	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6777739	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6779581	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6779671	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6787452	0.87[ASN][1000 genomes]
rs6788429	0.83[AMR][1000 genomes]
rs6797760	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6798462	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs6801373	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6803670	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806755	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633839	0.84[CEU][hapmap]
rs7634255	0.84[CEU][hapmap]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7610939	IFT80	cis	parietal	SCAN
rs7610939	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160385200-160395000	Weak transcription	Colonic Mucosa	Colon
2	chr3:160389400-160395200	Weak transcription	Pancreas	Pancrea
3	chr3:160389400-160395400	Weak transcription	Small Intestine	intestine
4	chr3:160390600-160393600	Enhancers	Stomach Mucosa	stomach
5	chr3:160391400-160394000	Enhancers	Liver	Liver
6	chr3:160391400-160395200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:160391600-160393600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:160392000-160394600	Enhancers	A549	lung
9	chr3:160392000-160395200	Weak transcription	HepG2	liver
10	chr3:160393200-160394000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr3:160393200-160394800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr3:160393400-160393600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:160393400-160393600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:160393400-160394600	Enhancers	Hela-S3	cervix
15	chr3:160393400-160394800	Enhancers	Duodenum Mucosa	Duodenum
16	chr3:160393400-160395000	Enhancers	Fetal Intestine Small	intestine
17	chr3:160393400-160395000	Enhancers	NHEK	skin
18	chr3:160393400-160395200	Enhancers	Fetal Intestine Large	intestine
19	chr3:160393400-160395800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:160393400-160395800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:160393400-160397000	Enhancers	HMEC	breast
22	chr3:160393400-160397200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:160393400-160397400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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