Variant report

Variant	rs877642
Chromosome Location	chr10:49788275-49788276
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:49776352..49778788-chr10:49787790..49790511,2	K562	blood:
2	chr10:49781506..49783468-chr10:49787135..49789633,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1075808	0.92[CEU][hapmap];0.85[JPT][hapmap];0.91[MKK][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1075809	1.00[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];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1075810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10776626	0.94[ASN][1000 genomes]
rs10857604	0.94[ASN][1000 genomes]
rs10857605	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1107998	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs11101388	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs11101389	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs12243298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12243359	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1345106	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7071547	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs7085667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7086059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7086075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7098855	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs877643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv550815	chr10:49774633-49794481	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv550816	chr10:49782417-49794481	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs877642	GPRIN2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49782800-49790200	Weak transcription	Aorta	Aorta
2	chr10:49783000-49788400	Enhancers	Primary B cells from cord blood	blood
3	chr10:49786200-49788400	Genic enhancers	NHLF	lung
4	chr10:49786200-49789000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:49786200-49789000	Enhancers	Colon Smooth Muscle	Colon
6	chr10:49786200-49792800	Enhancers	Brain Substantia Nigra	brain
7	chr10:49787000-49788400	Enhancers	NHDF-Ad	bronchial
8	chr10:49787000-49788800	Genic enhancers	Muscle Satellite Cultured Cells	--
9	chr10:49787000-49791800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr10:49787200-49788600	Enhancers	HMEC	breast
11	chr10:49787400-49788600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:49787400-49788600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr10:49787400-49788800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr10:49787600-49788400	Enhancers	Esophagus	oesophagus
15	chr10:49787600-49788400	Enhancers	HSMM	muscle
16	chr10:49787600-49788600	Enhancers	Ovary	ovary
17	chr10:49787600-49788800	Enhancers	Brain Anterior Caudate	brain
18	chr10:49787600-49788800	Enhancers	Rectal Smooth Muscle	rectum
19	chr10:49787600-49789400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr10:49787600-49790600	Enhancers	Brain Hippocampus Middle	brain
21	chr10:49787800-49788800	Enhancers	Brain Angular Gyrus	brain
22	chr10:49787800-49789000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr10:49787800-49791200	Weak transcription	Spleen	Spleen
24	chr10:49787800-49791400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:49787800-49792400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr10:49787800-49793200	Weak transcription	Gastric	stomach
27	chr10:49787800-49796800	Weak transcription	Right Atrium	heart
28	chr10:49788000-49788600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr10:49788000-49788800	Bivalent Enhancer	Fetal Stomach	stomach
30	chr10:49788000-49789000	Weak transcription	NH-A	brain
31	chr10:49788000-49789400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr10:49788000-49792600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr10:49788000-49792800	Strong transcription	HUVEC	blood vessel
34	chr10:49788000-49796000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr10:49788200-49788400	Enhancers	Adipose Nuclei	Adipose
36	chr10:49788200-49788800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr10:49788200-49788800	Genic enhancers	Brain Cingulate Gyrus	brain
38	chr10:49788200-49789800	Weak transcription	HSMMtube	muscle
39	chr10:49788200-49792200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:49788200-49792800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr10:49788200-49795600	Strong transcription	Osteobl	bone
42	chr10:49788200-49795800	Weak transcription	Monocytes-CD14+_RO01746	blood

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