Variant report

Variant	rs1866140
Chromosome Location	chr2:85921353-85921354
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10180391	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180445	0.82[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs10180451	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10180547	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10187164	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10187495	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10192752	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10203826	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10206121	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10210321	0.86[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs1030862	0.81[CEU][hapmap]
rs11127	0.82[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12620113	0.92[ASN][1000 genomes]
rs12714149	1.00[ASW][hapmap]
rs12845	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13389847	0.90[ASN][1000 genomes]
rs13408224	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1437742	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1437743	0.82[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1437744	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1437745	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1561284	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1561285	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1837115	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1866138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1866139	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1866141	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2043760	0.82[JPT][hapmap]
rs2070966	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2118402	0.87[ASN][1000 genomes]
rs2366805	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2366807	0.86[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2886767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2886768	0.88[ASN][1000 genomes]
rs34218330	0.90[ASN][1000 genomes]
rs34702373	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34771575	0.86[ASN][1000 genomes]
rs34943381	0.80[ASN][1000 genomes]
rs3755007	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4240200	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4240201	0.86[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4240202	0.86[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs4832181	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832183	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4832185	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4832187	0.80[ASN][1000 genomes]
rs55665393	0.81[ASN][1000 genomes]
rs59832218	0.82[ASN][1000 genomes]
rs61191323	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62163092	0.83[ASN][1000 genomes]
rs6740635	0.92[ASN][1000 genomes]
rs7585576	0.92[ASN][1000 genomes]
rs7908	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs880872	0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs934774	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv874465	chr2:85898898-85939207	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv2812	chr2:85899944-85929267	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv874466	chr2:85909026-85939207	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv874467	chr2:85916487-85946708	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1866140	GGCX	cis	parietal	SCAN
rs1866140	AC012454.4	cis	Whole Blood	GTEx
rs1866140	ATOH8	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85917000-85922800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:85918800-85921600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:85919600-85921600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:85919600-85921600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:85919600-85921600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:85920400-85924000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:85920400-85924600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:85920400-85925600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:85920600-85921400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:85920800-85921400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:85920800-85921600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:85920800-85921600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:85920800-85921600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr2:85921000-85921600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:85921000-85922000	Enhancers	HSMM	muscle
16	chr2:85921200-85921400	Enhancers	NHLF	lung
17	chr2:85921200-85922000	Enhancers	Lung	lung
18	chr2:85921200-85922400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:85921200-85922600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:85921200-85924400	Active TSS	Primary T cells fromperipheralblood	blood

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