Variant report

Variant	rs12529920
Chromosome Location	chr6:140301480-140301481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140296686..140298552-chr6:140300622..140302808,2	K562	blood:
2	chr6:139693406..139696942-chr6:140299260..140302508,7	MCF-7	breast:
3	chr6:140287936..140290734-chr6:140300872..140302631,2	K562	blood:
4	chr6:140299794..140302085-chr6:140302801..140306484,3	K562	blood:
5	chr6:139695460..139698700-chr6:140298901..140302123,4	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1028471	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10499219	0.86[EUR][1000 genomes]
rs11967326	0.87[AFR][1000 genomes]
rs12523886	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12528420	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12529701	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1572674	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17069706	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17069710	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17069727	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17069741	0.86[EUR][1000 genomes]
rs2050716	0.86[EUR][1000 genomes]
rs36026965	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60747543	0.85[EUR][1000 genomes]
rs62429482	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62429486	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62429513	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62429521	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62431062	0.86[EUR][1000 genomes]
rs62431064	0.86[EUR][1000 genomes]
rs62431065	0.86[EUR][1000 genomes]
rs62431066	0.84[EUR][1000 genomes]
rs6915764	0.83[EUR][1000 genomes]
rs73569508	0.91[AFR][1000 genomes]
rs73571530	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7770431	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9484329	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9484331	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9484332	0.86[EUR][1000 genomes];0.98[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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140291600-140302000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:140292600-140306000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:140295200-140303000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:140295400-140301800	Weak transcription	Aorta	Aorta
5	chr6:140295400-140302000	Weak transcription	Adipose Nuclei	Adipose
6	chr6:140295400-140302800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:140295400-140303000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:140295600-140302000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:140295600-140302600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:140295600-140303400	Weak transcription	Right Atrium	heart
11	chr6:140296400-140302600	Weak transcription	Fetal Lung	lung
12	chr6:140297000-140301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:140297400-140305800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:140298200-140303000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:140298200-140303000	Weak transcription	Pancreas	Pancrea
16	chr6:140298200-140305600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:140298200-140306200	Enhancers	Hela-S3	cervix
18	chr6:140298800-140305800	Enhancers	Osteobl	bone
19	chr6:140298800-140306000	Enhancers	NHLF	lung
20	chr6:140299200-140302000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:140299400-140301600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:140299400-140301600	Weak transcription	Fetal Intestine Small	intestine
23	chr6:140299400-140301800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:140299400-140301800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:140299400-140301800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:140299400-140301800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:140299400-140301800	Weak transcription	Ovary	ovary
28	chr6:140299400-140301800	Weak transcription	HMEC	breast
29	chr6:140299400-140302600	Weak transcription	Esophagus	oesophagus
30	chr6:140299400-140302800	Weak transcription	HUVEC	blood vessel
31	chr6:140299400-140303000	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:140299400-140303400	Weak transcription	Small Intestine	intestine
33	chr6:140299600-140301600	Weak transcription	Fetal Intestine Large	intestine
34	chr6:140299600-140302000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:140299600-140302000	Weak transcription	NHEK	skin
36	chr6:140299600-140302400	Weak transcription	A549	lung
37	chr6:140299600-140303200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:140299800-140301600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:140299800-140303400	Weak transcription	Liver	Liver
40	chr6:140300400-140305200	Enhancers	Fetal Kidney	kidney
41	chr6:140300400-140305600	Enhancers	Fetal Heart	heart
42	chr6:140300600-140301800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:140300600-140302000	Enhancers	Left Ventricle	heart
44	chr6:140300600-140302000	Enhancers	Psoas Muscle	Psoas
45	chr6:140300600-140303000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:140300600-140303200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:140300600-140304200	Enhancers	K562	blood
48	chr6:140300600-140305600	Enhancers	NH-A	brain
49	chr6:140300600-140305800	Enhancers	HSMM	muscle
50	chr6:140300600-140306600	Enhancers	Placenta	Placenta

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