Variant report

Variant	rs10931401
Chromosome Location	chr2:190039623-190039624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190039205..190041419-chr2:190045253..190047798,2	MCF-7	breast:
2	chr2:190036925..190039844-chr2:190040601..190043479,3	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10165127	0.89[EUR][1000 genomes]
rs10165257	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1016622	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10166385	0.92[ASN][1000 genomes]
rs10167242	0.83[ASN][1000 genomes]
rs10172607	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10173224	0.92[ASN][1000 genomes]
rs10184895	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10755002	0.90[ASN][1000 genomes]
rs10931403	0.90[ASN][1000 genomes]
rs10931405	0.88[ASN][1000 genomes]
rs10931411	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11901914	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12105389	0.81[JPT][hapmap]
rs12474942	0.96[ASN][1000 genomes]
rs12618316	0.92[EUR][1000 genomes]
rs12621657	0.85[ASN][1000 genomes]
rs12999125	0.92[ASN][1000 genomes]
rs13005714	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13005834	0.92[EUR][1000 genomes]
rs13006065	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13013089	0.92[EUR][1000 genomes]
rs13015183	0.89[ASN][1000 genomes]
rs13020999	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13024858	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13028226	0.94[ASN][1000 genomes]
rs13030984	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13408928	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13411992	0.92[ASN][1000 genomes]
rs13413518	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1356161	0.92[ASN][1000 genomes]
rs1356166	0.93[ASN][1000 genomes]
rs1399991	0.81[JPT][hapmap]
rs1464135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474000	0.85[ASN][1000 genomes]
rs1515864	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1515866	0.90[ASN][1000 genomes]
rs1515869	0.89[EUR][1000 genomes]
rs1533618	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1546617	0.92[ASN][1000 genomes]
rs1913892	0.92[ASN][1000 genomes]
rs1949327	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1973666	0.86[ASN][1000 genomes]
rs1983318	0.93[ASN][1000 genomes]
rs2138373	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2351631	0.90[ASN][1000 genomes]
rs2351632	0.95[ASN][1000 genomes]
rs2351633	0.91[ASN][1000 genomes]
rs2351635	0.86[ASN][1000 genomes]
rs36019389	0.90[EUR][1000 genomes]
rs4417749	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4667263	0.89[EUR][1000 genomes]
rs4667266	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs4667268	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4667270	0.92[ASN][1000 genomes]
rs4667271	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4667275	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62182417	0.83[EUR][1000 genomes]
rs6434324	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6434325	0.89[EUR][1000 genomes]
rs6434334	0.87[ASN][1000 genomes]
rs6434337	0.84[ASN][1000 genomes]
rs6704568	0.86[ASN][1000 genomes]
rs6728877	0.92[ASN][1000 genomes]
rs6732534	0.91[ASN][1000 genomes]
rs6741804	0.89[EUR][1000 genomes]
rs6749559	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6752781	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6761868	0.86[ASN][1000 genomes]
rs7560973	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7574281	0.84[ASN][1000 genomes]
rs7593860	0.89[EUR][1000 genomes]
rs7599222	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7603704	0.89[ASN][1000 genomes]
rs7606337	0.89[EUR][1000 genomes]
rs9288163	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.92[EUR][1000 genomes]
rs939158	0.86[ASN][1000 genomes]
rs939160	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10931401	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190019600-190040000	Weak transcription	Fetal Intestine Small	intestine
2	chr2:190029400-190040800	Weak transcription	Fetal Kidney	kidney
3	chr2:190029400-190042200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:190029600-190043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:190029800-190043200	Weak transcription	Psoas Muscle	Psoas
6	chr2:190030000-190041200	Weak transcription	HUVEC	blood vessel
7	chr2:190030200-190041200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:190030400-190043400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:190034000-190040800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:190034000-190043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:190034200-190041400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:190034800-190040400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:190036200-190040600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:190037000-190040400	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:190037000-190040400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:190037000-190040800	Weak transcription	Right Atrium	heart
17	chr2:190037000-190041000	Weak transcription	Ovary	ovary
18	chr2:190037200-190039800	Weak transcription	Adipose Nuclei	Adipose
19	chr2:190037200-190040600	Weak transcription	Fetal Lung	lung
20	chr2:190037400-190039800	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:190037400-190040400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:190037400-190040800	Weak transcription	Fetal Heart	heart
23	chr2:190037400-190040800	Weak transcription	Fetal Stomach	stomach
24	chr2:190037400-190041200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:190037400-190041400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:190037400-190042600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:190037400-190042600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:190038200-190039800	Strong transcription	NH-A	brain
29	chr2:190038600-190040000	Strong transcription	HSMM	muscle
30	chr2:190038600-190040000	Genic enhancers	NHDF-Ad	bronchial
31	chr2:190038600-190040600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:190038800-190039800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:190038800-190040200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:190038800-190040200	Genic enhancers	Osteobl	bone
35	chr2:190038800-190040600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:190038800-190040600	Genic enhancers	A549	lung
37	chr2:190038800-190040800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:190039000-190039800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:190039200-190040400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:190039200-190040800	Weak transcription	Aorta	Aorta
41	chr2:190039200-190040800	Weak transcription	NHLF	lung
42	chr2:190039400-190039800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:190039600-190040000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:190039600-190040000	Active TSS	HSMMtube	muscle
45	chr2:190039600-190040200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:190039600-190040600	Genic enhancers	Muscle Satellite Cultured Cells	--

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