Variant report

Variant	rs12665758
Chromosome Location	chr6:142541553-142541554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10485027	0.88[CEU][hapmap]
rs12661511	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs17071411	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17071541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804517	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811087	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap]
rs6931975	0.81[EUR][1000 genomes]
rs761155	0.81[EUR][1000 genomes]
rs9496261	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking 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 miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12665758	VTA1	cis	multi-tissue	Pritchard
rs12665758	VTA1	cis	lymphoblastoid	seeQTL
rs12665758	VTA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142489000-142543200	Weak transcription	Small Intestine	intestine
2	chr6:142496600-142546800	Weak transcription	NHLF	lung
3	chr6:142515400-142541800	Weak transcription	Psoas Muscle	Psoas
4	chr6:142519600-142541800	Strong transcription	HSMM	muscle
5	chr6:142521600-142542600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:142523000-142543000	Weak transcription	Stomach Mucosa	stomach
7	chr6:142532400-142543000	Weak transcription	Fetal Brain Male	brain
8	chr6:142533200-142543200	Weak transcription	HMEC	breast
9	chr6:142533800-142541600	Weak transcription	K562	blood
10	chr6:142534200-142541600	Weak transcription	Fetal Kidney	kidney
11	chr6:142534800-142543400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:142535000-142541600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:142535000-142541600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:142535000-142542000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:142535000-142542200	Weak transcription	Lung	lung
16	chr6:142535000-142542600	Weak transcription	Gastric	stomach
17	chr6:142535000-142543200	Weak transcription	NHEK	skin
18	chr6:142535000-142544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:142535000-142544800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:142535000-142545000	Weak transcription	Esophagus	oesophagus
21	chr6:142535000-142545600	Weak transcription	Aorta	Aorta
22	chr6:142535000-142548800	Weak transcription	NH-A	brain
23	chr6:142535200-142542000	Weak transcription	Hela-S3	cervix
24	chr6:142535200-142542400	Weak transcription	Ovary	ovary
25	chr6:142535200-142543400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:142535200-142544200	Weak transcription	Fetal Intestine Small	intestine
27	chr6:142535200-142545600	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:142535200-142546000	Weak transcription	Fetal Stomach	stomach
29	chr6:142535200-142548800	Weak transcription	Left Ventricle	heart
30	chr6:142535200-142552800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr6:142535400-142546800	Weak transcription	Fetal Intestine Large	intestine
32	chr6:142535600-142546200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr6:142535800-142541800	Weak transcription	Brain Germinal Matrix	brain
34	chr6:142535800-142542600	Weak transcription	HSMMtube	muscle
35	chr6:142535800-142543000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr6:142535800-142543400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:142535800-142553400	Weak transcription	Thymus	Thymus
38	chr6:142536000-142543800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:142536000-142544000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:142536000-142552800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:142536400-142543800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:142536400-142546600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:142536600-142541600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:142537000-142543600	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:142537600-142542400	Strong transcription	Primary B cells from cord blood	blood
46	chr6:142539200-142541600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:142539200-142541600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:142539200-142541600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr6:142539200-142541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:142539200-142542000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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