Variant report

Variant	rs12665886
Chromosome Location	chr7:16845751-16845752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr7:16845640-16845905	HepG2	liver:	n/a	n/a
2	MAFK	chr7:16845629-16845829	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:16792720..16796708-chr7:16843218..16846000,6	MCF-7	breast:
2	chr7:16821043..16823584-chr7:16844738..16846886,2	K562	blood:
3	chr7:16843443..16845247-chr7:16845405..16847405,2	MCF-7	breast:
4	chr7:16829970..16831887-chr7:16844780..16846882,2	K562	blood:
5	chr7:16842671..16846672-chr7:16872970..16875840,3	MCF-7	breast:

No data

Variant related genes	Relation type
AGR2	TF binding region
ENSG00000106541	Chromatin interaction
ENSG00000106537	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10085446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10224320	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10252977	0.95[ASN][1000 genomes]
rs10499476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12666607	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs12667956	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12672294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12674385	0.83[ASN][1000 genomes]
rs13229262	0.99[ASN][1000 genomes]
rs13437970	0.95[ASN][1000 genomes]
rs1525744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs17136670	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17150186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17629719	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1917742	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs28945075	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28945079	0.94[ASN][1000 genomes]
rs3757454	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807502	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807503	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817506	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817507	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817508	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817512	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[ASN][1000 genomes]
rs3823653	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55824063	0.99[ASN][1000 genomes]
rs56291875	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57997528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61130271	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62440423	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440424	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62440425	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440459	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73073559	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73078122	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73078127	0.83[ASN][1000 genomes]
rs73078130	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028125	chr7:16529160-16847225	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv887761	chr7:16834361-17732490	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv887762	chr7:16834361-17746628	Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv887763	chr7:16834361-17750811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv887764	chr7:16839835-17218800	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv887765	chr7:16839835-17750811	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 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	chr7:16843800-16845800	Enhancers	HepG2	liver
2	chr7:16844600-16854800	Weak transcription	Small Intestine	intestine
3	chr7:16844800-16847800	Weak transcription	Colonic Mucosa	Colon
4	chr7:16845000-16846000	Enhancers	Hela-S3	cervix
5	chr7:16845200-16845800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:16845400-16845800	Enhancers	NHEK	skin
7	chr7:16845400-16846000	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr7:16845400-16846200	Enhancers	Duodenum Mucosa	Duodenum
9	chr7:16845400-16846400	Enhancers	Stomach Mucosa	stomach
10	chr7:16845400-16846600	Enhancers	Fetal Intestine Small	intestine
11	chr7:16845400-16848400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr7:16845400-16852200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:16845400-16852800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:16845600-16846400	Enhancers	A549	lung
15	chr7:16845600-16846800	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links