Variant report

Variant	rs10187164
Chromosome Location	chr2:85928209-85928210
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:85839135..85840661-chr2:85928083..85930394,2	MCF-7	breast:
2	chr2:85919636..85921243-chr2:85926613..85928346,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168883	Chromatin interaction
ENSG00000168887	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10180391	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10180445	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180451	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180547	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187314	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10187495	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10192752	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203826	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206121	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10210321	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11127	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12620113	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12845	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13389847	0.82[ASN][1000 genomes]
rs13408224	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1437742	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1437743	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1437744	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1437745	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561284	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1561285	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1837115	0.96[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1866138	0.82[CHB][hapmap];0.96[JPT][hapmap]
rs1866139	0.87[CHB][hapmap];0.96[JPT][hapmap];0.85[ASN][1000 genomes]
rs1866140	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1866141	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2043760	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2070966	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2118402	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2366807	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2886767	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2886768	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34218330	0.83[ASN][1000 genomes]
rs34702373	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34943381	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35616630	0.88[EUR][1000 genomes]
rs4240200	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4240201	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4240202	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4832181	0.91[JPT][hapmap]
rs4832183	0.81[JPT][hapmap]
rs4832185	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4832187	0.83[ASN][1000 genomes]
rs55665393	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59832218	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61191323	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62163092	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6740635	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7585576	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7908	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs880872	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10187164	ATOH8	cis	Whole Blood	GTEx
rs10187164	AC012454.4	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85922000-85931400	Weak transcription	Lung	lung
2	chr2:85922400-85928600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:85924600-85928400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:85924600-85932200	Weak transcription	Spleen	Spleen
5	chr2:85925600-85930400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr2:85925800-85928400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:85926000-85931600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:85926000-85931600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:85926000-85932400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:85926000-85945200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr2:85926600-85929600	Weak transcription	Primary B cells from cord blood	blood
12	chr2:85926600-85932000	Weak transcription	K562	blood
13	chr2:85926800-85930200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:85927000-85928800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr2:85927200-85932400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:85927400-85929800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:85928000-85928800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr2:85928000-85928800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:85928000-85928800	Enhancers	A549	lung
20	chr2:85928000-85930400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:85928000-85930600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr2:85928000-85930600	Enhancers	NHDF-Ad	bronchial
23	chr2:85928000-85934800	Enhancers	Hela-S3	cervix
24	chr2:85928200-85928800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:85928200-85929200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr2:85928200-85929200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:85928200-85929800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:85928200-85930000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr2:85928200-85930000	Enhancers	NHLF	lung
30	chr2:85928200-85930200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr2:85928200-85930200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr2:85928200-85930200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:85928200-85930200	Enhancers	HMEC	breast

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