Variant report

Variant	rs17071541
Chromosome Location	chr6:142538823-142538824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10485027	0.88[CEU][hapmap];1.00[AFR][1000 genomes]
rs12661511	0.92[CHB][hapmap]
rs12665758	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]
rs17071411	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs17071423	1.00[AFR][1000 genomes]
rs1835	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]
rs3804517	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811087	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6931975	0.81[EUR][1000 genomes]
rs761155	0.81[EUR][1000 genomes]
rs9496261	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17071541	VTA1	cis	multi-tissue	Pritchard
rs17071541	VTA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

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	chr6:142534800-142539600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:142534800-142543400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:142535000-142539200	Weak transcription	Brain Angular Gyrus	brain
14	chr6:142535000-142539200	Weak transcription	Brain Anterior Caudate	brain
15	chr6:142535000-142539200	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:142535000-142539200	Weak transcription	Brain Substantia Nigra	brain
17	chr6:142535000-142539400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:142535000-142539600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:142535000-142539600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:142535000-142540200	Weak transcription	Colonic Mucosa	Colon
21	chr6:142535000-142540800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:142535000-142541400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr6:142535000-142541600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:142535000-142541600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:142535000-142542000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:142535000-142542200	Weak transcription	Lung	lung
27	chr6:142535000-142542600	Weak transcription	Gastric	stomach
28	chr6:142535000-142543200	Weak transcription	NHEK	skin
29	chr6:142535000-142544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:142535000-142544800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:142535000-142545000	Weak transcription	Esophagus	oesophagus
32	chr6:142535000-142545600	Weak transcription	Aorta	Aorta
33	chr6:142535000-142548800	Weak transcription	NH-A	brain
34	chr6:142535200-142539000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:142535200-142539200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:142535200-142539200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:142535200-142539200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:142535200-142539200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:142535200-142539200	Weak transcription	Fetal Lung	lung
40	chr6:142535200-142539200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:142535200-142539400	Weak transcription	Placenta	Placenta
42	chr6:142535200-142539600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:142535200-142539600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:142535200-142539600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:142535200-142539600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:142535200-142539600	Weak transcription	Dnd41	blood
47	chr6:142535200-142539800	Weak transcription	NHDF-Ad	bronchial
48	chr6:142535200-142541000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:142535200-142541000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:142535200-142542000	Weak transcription	Hela-S3	cervix

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