Variant report

Variant	rs3790508
Chromosome Location	chr1:151675486-151675487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151668533..151670449-chr1:151674606..151677478,3	MCF-7	breast:
2	chr1:151430268..151431777-chr1:151675061..151677444,2	MCF-7	breast:
3	chr1:151671136..151674505-chr1:151674889..151678422,3	K562	blood:
4	chr1:151674334..151676569-chr1:151677711..151679757,3	MCF-7	breast:
5	chr1:151671136..151673707-chr1:151674889..151677650,3	K562	blood:
6	chr1:151674905..151676971-chr1:151691184..151693969,2	MCF-7	breast:
7	chr1:151674632..151676262-chr1:151762381..151764969,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143442	Chromatin interaction
ENSG00000203288	Chromatin interaction
ENSG00000182134	Chromatin interaction
ENSG00000227045	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1196360	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs12130368	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12145098	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1781416	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs2280474	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3790508	RAB15	trans	lymphoblastoid	seeQTL
rs3790508	CGN	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151627400-151676000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:151638600-151675600	Weak transcription	Psoas Muscle	Psoas
3	chr1:151654800-151678000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:151663200-151677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:151663200-151683200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:151665400-151676400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:151666000-151685400	Weak transcription	A549	lung
8	chr1:151666400-151675800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:151666600-151676000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:151667000-151687400	Weak transcription	K562	blood
11	chr1:151667800-151686000	Weak transcription	HMEC	breast
12	chr1:151669600-151681200	Strong transcription	Fetal Brain Female	brain
13	chr1:151670000-151676800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:151670000-151689800	Weak transcription	Pancreas	Pancrea
15	chr1:151670400-151675600	Weak transcription	Fetal Brain Male	brain
16	chr1:151671200-151675800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:151671400-151682600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:151672000-151678000	Weak transcription	Stomach Mucosa	stomach
19	chr1:151672200-151680400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:151672400-151684800	Weak transcription	Small Intestine	intestine
21	chr1:151672800-151678400	Weak transcription	Colonic Mucosa	Colon
22	chr1:151673000-151675600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:151673000-151675600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:151673200-151675800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:151673200-151677000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:151673600-151678600	Strong transcription	Brain Germinal Matrix	brain
27	chr1:151673800-151676400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:151673800-151677000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:151673800-151680400	Strong transcription	Fetal Intestine Large	intestine
30	chr1:151673800-151682400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:151673800-151685200	Weak transcription	Fetal Kidney	kidney
32	chr1:151674000-151676000	Strong transcription	Fetal Intestine Small	intestine
33	chr1:151674000-151676400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:151674000-151677000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:151674000-151677200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:151674000-151677400	Weak transcription	Osteobl	bone
37	chr1:151674000-151677800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:151674000-151677800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:151674000-151678000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:151674000-151678600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:151674000-151682400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:151674000-151685400	Weak transcription	Gastric	stomach
43	chr1:151674200-151675600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:151674200-151675800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:151674200-151675800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:151674200-151675800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:151674200-151677600	Weak transcription	NHLF	lung
48	chr1:151674200-151677800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:151674200-151679800	Weak transcription	Right Ventricle	heart
50	chr1:151674200-151683200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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