Variant report

Variant	rs12140170
Chromosome Location	chr1:85849723-85849724
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	chr1:85839312..85843099-chr1:85847023..85851233,3	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10158674	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10782550	0.90[ASN][1000 genomes]
rs11161597	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161599	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161614	0.87[EUR][1000 genomes]
rs11801146	0.87[ASN][1000 genomes]
rs12118950	0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12120551	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12122816	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12123745	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12125900	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12128907	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12129502	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12130145	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12130380	0.86[EUR][1000 genomes]
rs12130591	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12131926	0.89[EUR][1000 genomes]
rs12132677	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12133722	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12135333	0.90[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12138621	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12138852	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12139958	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12140272	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12140457	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12140935	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12717763	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12724823	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12736004	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12743049	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12758237	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12758768	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498374	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1608536	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17384381	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17388521	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2076699	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2300639	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2300640	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28529751	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34561661	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35193119	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35240561	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35761966	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs36110608	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768223	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71652696	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85839800-85864200	Weak transcription	Aorta	Aorta
2	chr1:85841200-85851400	Weak transcription	Pancreas	Pancrea
3	chr1:85841200-85859800	Weak transcription	NH-A	brain
4	chr1:85842000-85850800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:85845000-85852800	Strong transcription	Osteobl	bone
6	chr1:85845000-85870000	Weak transcription	HSMMtube	muscle
7	chr1:85845800-85859800	Weak transcription	NHLF	lung
8	chr1:85846200-85852800	Strong transcription	HSMM	muscle
9	chr1:85846400-85850400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:85847200-85850200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:85847800-85850000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:85848400-85850800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:85848600-85851600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:85849000-85850200	Strong transcription	NHDF-Ad	bronchial
15	chr1:85849000-85852000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:85849200-85849800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:85849200-85853000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:85849400-85850000	Weak transcription	HUVEC	blood vessel
19	chr1:85849400-85850400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:85849400-85861600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:85849400-85863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:85849600-85850200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:85849600-85852000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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