Variant report

Variant	rs6956163
Chromosome Location	chr7:107987319-107987320
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:107876529..107879004-chr7:107987282..107988913,2	MCF-7	breast:
2	chr7:107862352..107865587-chr7:107986497..107989466,3	MCF-7	breast:
3	chr7:107952740..107955319-chr7:107986320..107988713,2	K562	blood:
4	chr7:107978588..107983755-chr7:107986747..107990779,6	MCF-7	breast:
5	chr7:107985603..107987833-chr7:107991095..107992631,2	K562	blood:
6	chr7:107984388..107993798-chr7:108093279..108099270,17	MCF-7	breast:
7	chr7:107841839..107843795-chr7:107987089..107988899,2	MCF-7	breast:
8	chr7:107893481..107895284-chr7:107986919..107989502,2	MCF-7	breast:
9	chr7:107936793..107941797-chr7:107984945..107993863,13	MCF-7	breast:
10	chr7:107940207..107942755-chr7:107985046..107987339,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1016148	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10487850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10953563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953568	0.85[EUR][1000 genomes]
rs11763042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769966	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12538050	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12673082	0.86[CEU][hapmap]
rs12673676	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs12705448	0.94[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13221333	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13242951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13243381	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17155485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17155518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17155522	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2098419	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300024	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300030	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34025892	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4142283	0.94[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4727703	0.94[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs7778203	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs969708	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1019059	chr7:107935905-107995523	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1021783	chr7:107935905-107998281	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv2761354	chr7:107935905-107998293	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv1031824	chr7:107935905-108006038	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1017288	chr7:107939739-108000837	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6956163	U3	cis	Thyroid	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107969000-107988200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:107975200-107989000	Weak transcription	Right Atrium	heart
3	chr7:107976800-107988400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:107977200-107988200	Weak transcription	A549	lung
5	chr7:107983200-107988200	Weak transcription	Pancreas	Pancrea
6	chr7:107983600-107988200	Weak transcription	Placenta	Placenta
7	chr7:107986000-107988800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr7:107986000-107988800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr7:107986000-107989000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr7:107986200-107987400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr7:107986200-107989000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:107986400-107988000	Weak transcription	Brain Anterior Caudate	brain
13	chr7:107986400-107988200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr7:107986600-107987800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:107986600-107988000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:107986600-107988000	Weak transcription	HepG2	liver
17	chr7:107986600-107988600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:107986600-107998200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr7:107986800-107987800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:107986800-107988000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr7:107986800-107988400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:107987000-107987400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:107987000-107988000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:107987200-107988200	Weak transcription	Brain Angular Gyrus	brain
25	chr7:107987200-107988400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:107987200-107988400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr7:107987200-107988600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links