Variant report

Variant	rs10747971
Chromosome Location	chr12:40402776-40402777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:40400651..40403072-chr12:40497922..40501179,3	MCF-7	breast:
2	12:40402537-40410050..12:40703633-40711447	GM12878	blood:
3	12:40402537-40410050..12:40497414-40501128	K562	blood:
4	chr12:40399921..40402831-chr12:40405268..40407402,2	MCF-7	breast:
5	12:40402537-40410050..12:40687302-40691796	GM12878	blood:
6	chr12:40401380..40404194-chr12:40458458..40460119,2	K562	blood:
7	12:40402537-40410050..12:40793507-40812339	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction
ENSG00000205592	Chromatin interaction
ENSG00000151229	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10784338	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10784353	0.92[JPT][hapmap]
rs10784356	0.92[JPT][hapmap]
rs10784359	0.84[JPT][hapmap]
rs10784369	0.92[JPT][hapmap]
rs10877891	0.84[JPT][hapmap]
rs10877990	0.84[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs10878049	0.84[JPT][hapmap]
rs10878089	0.84[JPT][hapmap]
rs11174609	0.84[JPT][hapmap]
rs11174670	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11175024	0.84[JPT][hapmap]
rs12813098	0.84[JPT][hapmap]
rs12823555	0.84[JPT][hapmap]
rs1482281	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1482283	0.89[ASW][hapmap];0.82[YRI][hapmap]
rs1586038	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs1600866	0.92[JPT][hapmap]
rs1813122	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2128277	0.84[JPT][hapmap]
rs2404352	0.92[JPT][hapmap]
rs2896825	0.92[JPT][hapmap]
rs3925535	0.84[JPT][hapmap]
rs4768200	0.81[JPT][hapmap]
rs530602	0.84[JPT][hapmap]
rs550669	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs555740	0.84[JPT][hapmap]
rs6581504	0.84[JPT][hapmap]
rs6650226	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs716268	0.84[JPT][hapmap]
rs7313209	0.84[JPT][hapmap]
rs7313231	0.84[JPT][hapmap]
rs7953129	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs7954875	0.95[CHB][hapmap];0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7959498	0.84[JPT][hapmap]
rs7960662	0.92[JPT][hapmap]
rs7964150	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7970812	0.84[JPT][hapmap]
rs9669240	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1052202	chr12:40322607-40406760	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40384400-40405200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:40384400-40405400	Weak transcription	Pancreas	Pancrea
3	chr12:40393400-40405400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:40394000-40405400	Weak transcription	Left Ventricle	heart
5	chr12:40394000-40410800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:40394200-40403800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:40394400-40405000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:40394400-40405200	Weak transcription	Hela-S3	cervix
9	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:40395200-40405400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:40402200-40425600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links