Variant report

Variant	rs2495392
Chromosome Location	chr1:151677249-151677250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151511777..151514221-chr1:151676659..151678306,2	MCF-7	breast:
2	chr1:151668533..151670449-chr1:151674606..151677478,3	MCF-7	breast:
3	chr1:151430268..151431777-chr1:151675061..151677444,2	MCF-7	breast:
4	chr1:151671136..151674505-chr1:151674889..151678422,3	K562	blood:
5	chr1:151671136..151673707-chr1:151674889..151677650,3	K562	blood:

Variant related genes	Relation type
ENSG00000232536	Chromatin interaction
ENSG00000227045	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143442	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1048694	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10888428	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204866	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11586679	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1196350	0.80[MEX][hapmap]
rs1196352	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1196357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs1196459	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1196464	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1196465	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1201651	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1211981	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12122920	0.84[MEX][hapmap]
rs1308137	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1308139	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1308143	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1308145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1308146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1308147	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1308148	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1308152	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1308158	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1717128	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17641780	0.92[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1781434	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1891589	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2460996	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2489892	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2495393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2495394	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3204344	0.96[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs35981950	0.83[EUR][1000 genomes]
rs3790512	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6684548	0.95[EUR][1000 genomes]
rs6685067	0.96[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6687866	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs6702842	0.95[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7534887	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2495392	BCL9	cis	cerebellum	SCAN
rs2495392	TDRKH	cis	cerebellum	SCAN
rs2495392	PLEKHO1	cis	cerebellum	SCAN
rs2495392	LINGO4	cis	cerebellum	SCAN
rs2495392	LCE1C	cis	parietal	SCAN
rs2495392	TDRKH	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151654800-151678000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:151663200-151677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:151663200-151683200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:151666000-151685400	Weak transcription	A549	lung
5	chr1:151667000-151687400	Weak transcription	K562	blood
6	chr1:151667800-151686000	Weak transcription	HMEC	breast
7	chr1:151669600-151681200	Strong transcription	Fetal Brain Female	brain
8	chr1:151670000-151689800	Weak transcription	Pancreas	Pancrea
9	chr1:151671400-151682600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:151672000-151678000	Weak transcription	Stomach Mucosa	stomach
11	chr1:151672200-151680400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:151672400-151684800	Weak transcription	Small Intestine	intestine
13	chr1:151672800-151678400	Weak transcription	Colonic Mucosa	Colon
14	chr1:151673600-151678600	Strong transcription	Brain Germinal Matrix	brain
15	chr1:151673800-151680400	Strong transcription	Fetal Intestine Large	intestine
16	chr1:151673800-151682400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:151673800-151685200	Weak transcription	Fetal Kidney	kidney
18	chr1:151674000-151677400	Weak transcription	Osteobl	bone
19	chr1:151674000-151677800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:151674000-151677800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:151674000-151678000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:151674000-151678600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:151674000-151682400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:151674000-151685400	Weak transcription	Gastric	stomach
25	chr1:151674200-151677600	Weak transcription	NHLF	lung
26	chr1:151674200-151677800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:151674200-151679800	Weak transcription	Right Ventricle	heart
28	chr1:151674200-151683200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:151674200-151683200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:151674200-151687400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:151674400-151677600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:151674400-151677800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:151674400-151679400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:151674600-151677400	Weak transcription	Adipose Nuclei	Adipose
35	chr1:151674600-151677800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:151674600-151678000	Weak transcription	HSMM	muscle
37	chr1:151674600-151678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:151674600-151678400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:151674600-151678600	Weak transcription	Lung	lung
40	chr1:151674600-151681800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:151674600-151682400	Weak transcription	Brain Substantia Nigra	brain
42	chr1:151674600-151682600	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:151674600-151683200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:151674600-151683200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:151674600-151685200	Weak transcription	Fetal Lung	lung
46	chr1:151674600-151686000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:151674800-151677400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:151674800-151677400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:151674800-151677400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:151674800-151677400	Weak transcription	Placenta	Placenta

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