Variant report

Variant	rs939160
Chromosome Location	chr2:190074622-190074623
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190074579..190076225-chr2:190085427..190087119,2	MCF-7	breast:
2	chr2:190068274..190071014-chr2:190073430..190076156,3	K562	blood:
3	chr2:190064765..190067723-chr2:190072988..190074631,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10165257	0.92[ASN][1000 genomes]
rs10166385	0.94[ASN][1000 genomes]
rs10167242	0.85[ASN][1000 genomes]
rs10172607	0.93[ASN][1000 genomes]
rs10173224	0.95[ASN][1000 genomes]
rs10184895	0.93[ASN][1000 genomes]
rs10755002	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10931401	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10931403	0.93[ASN][1000 genomes]
rs10931404	0.84[AFR][1000 genomes]
rs10931405	0.87[ASN][1000 genomes]
rs10931411	0.81[ASN][1000 genomes]
rs11901914	0.93[ASN][1000 genomes]
rs12105389	0.90[YRI][hapmap]
rs12474942	0.92[ASN][1000 genomes]
rs12621657	0.85[ASN][1000 genomes]
rs12999122	0.89[AFR][1000 genomes]
rs12999125	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13006065	0.91[ASN][1000 genomes]
rs13012327	0.85[AFR][1000 genomes]
rs13015183	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13018252	0.94[JPT][hapmap]
rs13028226	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13031211	0.80[JPT][hapmap];0.93[YRI][hapmap]
rs13031609	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13408928	0.95[ASN][1000 genomes]
rs13411992	0.96[ASN][1000 genomes]
rs13413518	0.95[ASN][1000 genomes]
rs1356161	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1356165	0.92[YRI][hapmap]
rs1356166	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1356167	0.87[YRI][hapmap]
rs1356168	0.86[YRI][hapmap]
rs1399991	0.90[YRI][hapmap]
rs1399992	0.87[AFR][1000 genomes]
rs1464135	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1474000	0.86[ASN][1000 genomes]
rs1515866	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1515874	0.86[AFR][1000 genomes]
rs1520858	0.95[JPT][hapmap]
rs1533618	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1546617	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1913892	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1973666	0.93[ASN][1000 genomes]
rs1983318	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2351631	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2351632	0.93[ASN][1000 genomes]
rs2351633	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2351635	0.84[ASN][1000 genomes]
rs35772309	0.81[AFR][1000 genomes]
rs4667268	0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs4667270	0.95[ASN][1000 genomes]
rs4667271	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4667275	0.84[ASN][1000 genomes]
rs6434334	0.88[ASN][1000 genomes]
rs6434337	0.85[ASN][1000 genomes]
rs6704568	0.85[ASN][1000 genomes]
rs6728877	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6732534	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6761868	0.85[ASN][1000 genomes]
rs7419888	0.93[YRI][hapmap]
rs7574281	0.86[ASN][1000 genomes]
rs7587147	0.87[AFR][1000 genomes]
rs7587956	0.89[AFR][1000 genomes]
rs7599222	0.96[ASN][1000 genomes]
rs7603704	0.90[ASN][1000 genomes]
rs939158	0.84[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
rs939160	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190071200-190075000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:190072200-190074800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:190072600-190074800	Enhancers	Adipose Nuclei	Adipose
4	chr2:190072600-190076000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:190072800-190074800	Enhancers	HUVEC	blood vessel
6	chr2:190072800-190074800	Enhancers	NHLF	lung
7	chr2:190072800-190075000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:190072800-190075800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:190073000-190075400	Enhancers	Hela-S3	cervix
10	chr2:190073000-190077000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:190073000-190077000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:190073200-190074800	Enhancers	NH-A	brain
13	chr2:190073200-190075400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr2:190073200-190075400	Enhancers	Fetal Stomach	stomach
15	chr2:190073200-190075400	Enhancers	HSMM	muscle
16	chr2:190073200-190075800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:190073200-190077000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:190073400-190074800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:190073400-190074800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:190073400-190077000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr2:190073600-190075400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:190073600-190076600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:190073800-190074800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:190073800-190075400	Weak transcription	Aorta	Aorta
25	chr2:190073800-190075400	Weak transcription	Ovary	ovary
26	chr2:190073800-190075400	Weak transcription	K562	blood
27	chr2:190073800-190075800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:190074000-190075800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:190074000-190076000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:190074000-190079400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:190074200-190075000	Flanking Active TSS	A549	lung
32	chr2:190074200-190076000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr2:190074200-190076000	Enhancers	Rectal Smooth Muscle	rectum
34	chr2:190074200-190076200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr2:190074400-190074800	Enhancers	Fetal Lung	lung
36	chr2:190074400-190075000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr2:190074400-190075800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:190074400-190076000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:190074600-190074800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:190074600-190074800	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr2:190074600-190074800	Active TSS	HSMMtube	muscle
42	chr2:190074600-190074800	Flanking Active TSS	NHEK	skin
43	chr2:190074600-190075000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:190074600-190075000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:190074600-190075000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:190074600-190075000	Flanking Active TSS	NHDF-Ad	bronchial
47	chr2:190074600-190075000	Flanking Active TSS	Osteobl	bone
48	chr2:190074600-190075400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:190074600-190075800	Enhancers	Brain Hippocampus Middle	brain
50	chr2:190074600-190076000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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