Variant report

Variant	rs10173957
Chromosome Location	chr2:47504611-47504612
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47497455..47500389-chr2:47501805..47505272,3	MCF-7	breast:
2	chr2:47394132..47407926-chr2:47492481..47507054,74	K562	blood:
3	chr2:47397474..47405591-chr2:47490090..47505751,58	MCF-7	breast:
4	chr2:47299206..47300980-chr2:47503674..47506329,2	MCF-7	breast:
5	chr2:47400556..47404810-chr2:47503337..47507243,8	K562	blood:
6	chr2:47401793..47405586-chr2:47504397..47507679,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10165172	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10165417	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10168183	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10176620	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181882	0.88[AMR][1000 genomes]
rs10189331	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191879	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10201528	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204097	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204159	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204202	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383554	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13383788	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384033	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13386635	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387191	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408016	0.93[EUR][1000 genomes]
rs13412502	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412948	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13413278	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13422346	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13422784	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28851944	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56057658	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58176408	0.93[EUR][1000 genomes]
rs59937171	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806460	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72806465	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806485	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806489	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73926815	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47499600-47514400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:47500000-47511800	Weak transcription	Thymus	Thymus
3	chr2:47500600-47506600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:47500800-47508800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:47501400-47505000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:47501400-47516000	Weak transcription	Stomach Mucosa	stomach
7	chr2:47502000-47509600	Weak transcription	A549	lung
8	chr2:47502000-47517200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:47502600-47509600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:47502600-47513000	Weak transcription	Brain Anterior Caudate	brain
11	chr2:47503600-47510600	Weak transcription	Brain Substantia Nigra	brain
12	chr2:47503600-47511800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:47503800-47505000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:47504000-47504800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:47504000-47504800	Enhancers	NHEK	skin
16	chr2:47504000-47505000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:47504000-47505000	Enhancers	HMEC	breast
18	chr2:47504000-47505200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:47504200-47509400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:47504400-47509400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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