Variant report

Variant	rs10931411
Chromosome Location	chr2:190139879-190139880
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	chr2:190085609..190089806-chr2:190139492..190143052,4	MCF-7	breast:
2	chr2:190139713..190141267-chr2:190148148..190150261,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10165257	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1016622	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10166385	0.83[ASN][1000 genomes]
rs10167242	0.89[ASN][1000 genomes]
rs10172607	0.87[ASN][1000 genomes]
rs10173224	0.85[ASN][1000 genomes]
rs10184895	0.87[ASN][1000 genomes]
rs10188246	0.85[ASN][1000 genomes]
rs10207812	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs10755002	0.81[ASN][1000 genomes]
rs10931401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10931403	0.88[ASN][1000 genomes]
rs10931405	0.93[ASN][1000 genomes]
rs11676905	0.85[ASN][1000 genomes]
rs11901914	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12474942	0.85[ASN][1000 genomes]
rs12618316	0.82[EUR][1000 genomes]
rs12621657	0.96[ASN][1000 genomes]
rs12994482	0.85[ASN][1000 genomes]
rs12999125	0.84[ASN][1000 genomes]
rs13005714	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs13005834	0.82[EUR][1000 genomes]
rs13006065	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13013089	0.82[EUR][1000 genomes]
rs13015183	0.80[ASN][1000 genomes]
rs13018252	0.88[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap]
rs13020999	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13024858	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs13028226	0.82[ASN][1000 genomes]
rs13030984	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs13035381	0.87[EUR][1000 genomes]
rs13408928	0.84[ASN][1000 genomes]
rs13411992	0.85[ASN][1000 genomes]
rs13413518	0.84[ASN][1000 genomes]
rs1356161	0.85[ASN][1000 genomes]
rs1356166	0.83[ASN][1000 genomes]
rs1464135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1474000	0.94[ASN][1000 genomes]
rs1515864	1.00[CEU][hapmap]
rs1515866	0.81[ASN][1000 genomes]
rs1520854	1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap]
rs1520856	0.84[EUR][1000 genomes]
rs1520858	0.89[CEU][hapmap];0.88[JPT][hapmap]
rs1533618	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1546617	0.83[ASN][1000 genomes]
rs1851104	1.00[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs1913892	0.85[ASN][1000 genomes]
rs1949327	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs1983318	0.83[ASN][1000 genomes]
rs1992295	1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap]
rs2138373	1.00[CEU][hapmap]
rs2351631	0.81[ASN][1000 genomes]
rs2351632	0.86[ASN][1000 genomes]
rs2351633	0.82[ASN][1000 genomes]
rs2351635	0.97[ASN][1000 genomes]
rs2351932	0.82[ASN][1000 genomes]
rs2683012	0.82[ASN][1000 genomes]
rs36019389	0.80[EUR][1000 genomes]
rs4417749	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs4667266	1.00[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4667268	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4667270	0.84[ASN][1000 genomes]
rs4667271	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4667275	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6434322	0.84[CHD][hapmap]
rs6434324	1.00[CEU][hapmap]
rs6434334	0.93[ASN][1000 genomes]
rs6434337	0.95[ASN][1000 genomes]
rs6434343	1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap]
rs6704568	0.95[ASN][1000 genomes]
rs6728877	0.82[ASN][1000 genomes]
rs6732534	0.84[ASN][1000 genomes]
rs6749559	1.00[CEU][hapmap]
rs6752781	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6761868	0.95[ASN][1000 genomes]
rs7422875	0.85[ASN][1000 genomes]
rs7425383	0.85[ASN][1000 genomes]
rs7556928	0.87[EUR][1000 genomes]
rs7560973	1.00[CEU][hapmap]
rs7574281	0.94[ASN][1000 genomes]
rs7599222	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7603704	0.89[ASN][1000 genomes]
rs9288163	1.00[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs939158	0.97[ASN][1000 genomes]
rs939160	0.81[ASN][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875614	chr2:190110841-190254758	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10931411	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190133200-190140800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:190133800-190140600	Weak transcription	NHDF-Ad	bronchial
3	chr2:190134200-190140400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:190139000-190141400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:190139200-190140000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:190139200-190140600	Weak transcription	NHEK	skin
7	chr2:190139200-190145400	Weak transcription	Fetal Lung	lung
8	chr2:190139400-190140400	Weak transcription	A549	lung
9	chr2:190139400-190140600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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