Variant report

Variant	rs12529188
Chromosome Location	chr6:140665872-140665873
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	chr6:140661443..140663536-chr6:140664188..140666341,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1113096	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11965946	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966793	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11967431	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11969633	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12524727	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12525793	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12526277	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12529620	0.82[ASN][1000 genomes]
rs12529729	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1390500	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1496114	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1580734	0.82[ASN][1000 genomes]
rs17069805	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17069893	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17069935	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069970	0.91[ASN][1000 genomes]
rs1879097	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2328026	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2328060	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57789174	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59447713	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62429779	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62429786	0.97[ASN][1000 genomes]
rs62429787	0.97[ASN][1000 genomes]
rs62429788	0.97[ASN][1000 genomes]
rs62429789	0.97[ASN][1000 genomes]
rs62429831	0.85[ASN][1000 genomes]
rs62431098	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62431099	0.82[EUR][1000 genomes]
rs62431110	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62431142	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6914407	0.97[ASN][1000 genomes]
rs732015	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[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	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015293	chr6:140544956-140798437	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv817390	chr6:140558103-141166039	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12529188	UTRN	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140660000-140670400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:140664400-140669400	Enhancers	HUVEC	blood vessel
3	chr6:140665000-140666000	Enhancers	Fetal Heart	heart
4	chr6:140665000-140666200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:140665000-140666200	Enhancers	NHEK	skin
6	chr6:140665000-140667000	Enhancers	NHDF-Ad	bronchial
7	chr6:140665000-140668000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:140665200-140666000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:140665200-140666200	Enhancers	HMEC	breast
10	chr6:140665200-140667000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:140665200-140667000	Enhancers	Osteobl	bone
12	chr6:140665200-140668600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:140665200-140669000	Enhancers	NHLF	lung
14	chr6:140665400-140666000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:140665400-140666200	Enhancers	NH-A	brain
16	chr6:140665400-140667000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:140665400-140668000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:140665400-140668400	Enhancers	HSMM	muscle
19	chr6:140665600-140666600	Weak transcription	Liver	Liver
20	chr6:140665600-140668800	Enhancers	HSMMtube	muscle
21	chr6:140665800-140666000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:140665800-140666200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:140665800-140666200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:140665800-140666200	Enhancers	Hela-S3	cervix

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