Variant report

Variant	rs12139958
Chromosome Location	chr1:85842112-85842113
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: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10782550	0.82[ASN][1000 genomes]
rs11161597	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11161599	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11161614	0.87[EUR][1000 genomes]
rs12118950	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12120551	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12122816	0.86[ASN][1000 genomes]
rs12123745	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12125900	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12128907	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12129502	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130145	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130380	0.86[EUR][1000 genomes]
rs12130591	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12131926	0.89[EUR][1000 genomes]
rs12132677	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12133722	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12135333	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12138621	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138852	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140170	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12140272	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12140457	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140935	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12717763	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12724823	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12736004	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12743049	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12758237	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12758768	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1498374	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1608536	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17384381	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17388521	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2076699	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2300639	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2300640	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28529751	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34561661	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35193119	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35240561	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35761966	0.86[ASN][1000 genomes]
rs36110608	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3768223	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71652696	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[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	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85834800-85844200	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:85836800-85843000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr1:85837200-85842400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:85837800-85842200	Enhancers	Rectal Smooth Muscle	rectum
5	chr1:85838200-85842800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:85838400-85842800	Enhancers	HUVEC	blood vessel
7	chr1:85838600-85843400	Weak transcription	Fetal Brain Female	brain
8	chr1:85838800-85842600	Enhancers	Colon Smooth Muscle	Colon
9	chr1:85839000-85842600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr1:85839000-85843600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:85839400-85846400	Weak transcription	Small Intestine	intestine
12	chr1:85839800-85842600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:85839800-85864200	Weak transcription	Aorta	Aorta
14	chr1:85840000-85844200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:85840000-85844200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:85840000-85844800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:85840000-85844800	Weak transcription	Ovary	ovary
18	chr1:85840000-85845200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:85840200-85844400	Weak transcription	HSMMtube	muscle
20	chr1:85840200-85844800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:85840200-85844800	Weak transcription	Fetal Stomach	stomach
22	chr1:85840200-85845200	Weak transcription	HepG2	liver
23	chr1:85840200-85845400	Weak transcription	NHLF	lung
24	chr1:85840200-85845600	Weak transcription	Psoas Muscle	Psoas
25	chr1:85840400-85845200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:85840400-85845200	Weak transcription	HSMM	muscle
27	chr1:85840400-85845400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:85840400-85848000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:85841000-85842600	Enhancers	A549	lung
30	chr1:85841200-85842200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr1:85841200-85842400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:85841200-85851400	Weak transcription	Pancreas	Pancrea
33	chr1:85841200-85859800	Weak transcription	NH-A	brain
34	chr1:85841400-85842400	Enhancers	Fetal Kidney	kidney
35	chr1:85841600-85844800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:85841800-85842800	Weak transcription	Osteobl	bone
37	chr1:85841800-85844800	Weak transcription	Brain Anterior Caudate	brain
38	chr1:85841800-85845000	Weak transcription	Fetal Intestine Small	intestine
39	chr1:85841800-85848000	Weak transcription	NHDF-Ad	bronchial
40	chr1:85842000-85844800	Weak transcription	Liver	Liver
41	chr1:85842000-85845200	Weak transcription	Fetal Lung	lung
42	chr1:85842000-85850800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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