Variant report

Variant	rs7592624
Chromosome Location	chr2:234602906-234602907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234599124..234606471-chr2:234613478..234621007,17	MCF-7	breast:
2	chr2:234473868..234476982-chr2:234602699..234604920,3	MCF-7	breast:
3	chr2:234473282..234477495-chr2:234598048..234603332,9	MCF-7	breast:
4	chr2:234388753..234400184-chr2:234596527..234603213,35	MCF-7	breast:
5	chr2:234393680..234401613-chr2:234597738..234605139,18	MCF-7	breast:
6	chr2:234597435..234606028-chr2:234613419..234620116,22	MCF-7	breast:
7	chr2:234387197..234390730-chr2:234600088..234603557,3	MCF-7	breast:
8	chr2:234355853..234357392-chr2:234601737..234604100,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000085982	Chromatin interaction
ENSG00000224814	Chromatin interaction
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10190976	1.00[ASW][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs10199293	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12477979	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12988520	0.96[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2602377	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2602378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2602379	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2602380	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2602381	0.92[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2741047	0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2741048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2741049	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2741050	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4433994	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs4583459	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4663888	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6707947	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6737107	1.00[JPT][hapmap]
rs6754100	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs6761246	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs71405710	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7579530	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7587916	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.98[ASN][1000 genomes]
rs7595138	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7592624	ALPI	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234597800-234608600	Weak transcription	Gastric	stomach
2	chr2:234599400-234608000	Weak transcription	HUVEC	blood vessel
3	chr2:234600400-234608200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:234600800-234603000	Weak transcription	Right Atrium	heart
5	chr2:234601400-234603000	Enhancers	Duodenum Mucosa	Duodenum
6	chr2:234601600-234603600	Flanking Active TSS	Liver	Liver
7	chr2:234602000-234603000	Transcr. at gene 5' and 3'	NHEK	skin
8	chr2:234602000-234603200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:234602200-234607600	Weak transcription	Pancreas	Pancrea
10	chr2:234602400-234604200	Enhancers	HepG2	liver
11	chr2:234602400-234604400	Enhancers	Hela-S3	cervix
12	chr2:234602600-234603400	Enhancers	Stomach Mucosa	stomach
13	chr2:234602800-234603000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:234602800-234603800	Enhancers	A549	lung
15	chr2:234602800-234614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links