Variant report

Variant	rs640512
Chromosome Location	chr7:26849660-26849661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10227140	0.81[AMR][1000 genomes]
rs10238253	0.81[AMR][1000 genomes]
rs10247509	0.81[AMR][1000 genomes]
rs10256799	0.81[AMR][1000 genomes]
rs10273468	0.81[AMR][1000 genomes]
rs12700761	0.81[AMR][1000 genomes]
rs1391805	0.90[YRI][hapmap]
rs213533	1.00[JPT][hapmap]
rs213536	1.00[JPT][hapmap]
rs2769364	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2769365	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34833677	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3801806	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3801835	0.90[ASN][1000 genomes]
rs3801860	0.81[AMR][1000 genomes]
rs4573150	0.81[AMR][1000 genomes]
rs471536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475238	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476098	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477924	1.00[JPT][hapmap];0.86[YRI][hapmap]
rs484426	0.82[EUR][1000 genomes]
rs490366	0.90[YRI][hapmap]
rs498561	0.81[EUR][1000 genomes]
rs503110	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs504955	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532320	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550141	0.90[YRI][hapmap]
rs556402	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564260	1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57027817	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570840	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs580904	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs591895	1.00[JPT][hapmap]
rs607099	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622011	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639221	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6461965	0.81[AMR][1000 genomes]
rs648297	0.81[EUR][1000 genomes]
rs659131	1.00[JPT][hapmap]
rs667841	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs673502	1.00[JPT][hapmap]
rs687603	0.83[EUR][1000 genomes]
rs688039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774367	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7784548	0.81[AMR][1000 genomes]
rs9648018	0.81[AMR][1000 genomes]
rs9648020	0.81[AMR][1000 genomes]
rs9648330	0.82[AMR][1000 genomes]
rs989250	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv887855	chr7:26823963-26872652	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs640512	HOTAIRM1	cis	Whole Blood	GTEx
rs640512	SKAP2	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26808000-26854800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:26813000-26871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:26825400-26872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:26839400-26871800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:26843200-26851800	Weak transcription	Fetal Lung	lung
6	chr7:26843600-26870800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:26843600-26871400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:26843800-26863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr7:26844400-26853200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:26845800-26851600	Weak transcription	GM12878-XiMat	blood
11	chr7:26846200-26850200	Strong transcription	Primary B cells from cord blood	blood
12	chr7:26846200-26850200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr7:26846800-26850000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:26847200-26853000	Weak transcription	Ovary	ovary
15	chr7:26847400-26853200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:26848200-26851000	Weak transcription	Lung	lung
17	chr7:26849000-26850400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr7:26849000-26850400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr7:26849400-26850000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:26849600-26850200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:26849600-26850400	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links