Variant report

Variant	rs1022878
Chromosome Location	chr10:28428926-28428927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10740782	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10826403	0.87[AFR][1000 genomes]
rs12241932	0.95[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1781830	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1781831	0.85[ASN][1000 genomes]
rs1892395	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1986268	0.95[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2607548	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2763315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2801845	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2801846	0.85[ASN][1000 genomes]
rs2887214	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2985512	0.82[ASN][1000 genomes]
rs2985516	0.85[ASN][1000 genomes]
rs2985524	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2985525	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2985529	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2985530	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2985533	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2997203	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2997208	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3890674	0.83[EUR][1000 genomes]
rs4747617	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6481509	0.85[ASN][1000 genomes]
rs6481510	0.85[ASN][1000 genomes]
rs7081423	0.85[ASN][1000 genomes]
rs7914949	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7920803	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9299599	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831816	chr10:28304698-28493635	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv831817	chr10:28369836-28539930	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1848511	chr10:28373644-28464753	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv894989	chr10:28384098-28449974	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv949151	chr10:28386125-28455221	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
11	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1022878	LOC387646	cis	parietal	SCAN
rs1022878	MYO3A	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28376000-28438400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr10:28403600-28443200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:28413200-28440600	Weak transcription	Left Ventricle	heart
4	chr10:28417000-28449200	Weak transcription	Pancreas	Pancrea
5	chr10:28417600-28458000	Weak transcription	Aorta	Aorta
6	chr10:28426400-28435800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr10:28426600-28431200	Enhancers	HUVEC	blood vessel
8	chr10:28426800-28438400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr10:28427000-28429200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:28427200-28438200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr10:28427200-28440600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:28427200-28448600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr10:28427400-28435600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:28427600-28431200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr10:28427600-28436000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr10:28428000-28435600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr10:28428200-28436000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr10:28428400-28434400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:28428400-28435600	Weak transcription	Primary T cells from cord blood	blood
20	chr10:28428400-28435800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:28428400-28435800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr10:28428600-28429200	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links