Variant report

Variant	rs4398471
Chromosome Location	chr3:142333969-142333970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142314581..142317142-chr3:142331753..142334464,2	MCF-7	breast:
2	chr3:142314791..142317138-chr3:142333698..142336127,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120756	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11711434	0.85[ASN][1000 genomes]
rs13316756	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17623058	0.84[ASN][1000 genomes]
rs2140433	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2140434	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2177397	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28365824	0.81[ASN][1000 genomes]
rs28378300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28647471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28709617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821647	0.85[CEU][hapmap]
rs4259003	0.85[CEU][hapmap]
rs4582093	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56161530	0.85[ASN][1000 genomes]
rs56383228	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58910647	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440095	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773213	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6778383	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs6797237	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797745	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6800573	1.00[CEU][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73228757	0.84[ASN][1000 genomes]
rs73228758	0.84[ASN][1000 genomes]
rs73228762	0.84[ASN][1000 genomes]
rs73228782	0.84[ASN][1000 genomes]
rs73240328	0.87[ASN][1000 genomes]
rs7622648	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7633021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647212	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9683274	0.92[ASN][1000 genomes]
rs9813377	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9816128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847445	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9851381	0.84[CEU][hapmap]
rs9857567	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9858204	0.88[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9862686	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9868309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142317200-142337600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:142317400-142337800	Weak transcription	HepG2	liver
3	chr3:142331000-142335200	Enhancers	Stomach Mucosa	stomach
4	chr3:142332000-142335600	Enhancers	Fetal Intestine Large	intestine
5	chr3:142332200-142335200	Enhancers	Fetal Intestine Small	intestine
6	chr3:142332600-142335000	Enhancers	A549	lung
7	chr3:142332800-142335000	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr3:142333000-142334600	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr3:142333000-142334800	Enhancers	Duodenum Mucosa	Duodenum
10	chr3:142333200-142334000	Enhancers	Colonic Mucosa	Colon
11	chr3:142333200-142337600	Weak transcription	HMEC	breast
12	chr3:142333200-142337600	Weak transcription	NHEK	skin
13	chr3:142333400-142335000	Enhancers	Small Intestine	intestine
14	chr3:142333600-142335000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr3:142333800-142334000	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links