Variant report

Variant	rs12052514
Chromosome Location	chr2:191378170-191378171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10084203	0.81[ASN][1000 genomes]
rs10174174	0.82[ASN][1000 genomes]
rs10188341	0.84[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10190082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10197348	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs10432434	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931458	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1128723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11885992	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12053190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470863	0.80[ASN][1000 genomes]
rs12472081	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12477369	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12693579	0.94[ASN][1000 genomes]
rs13417431	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16832765	0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2192010	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35818159	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129082	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4258824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4261750	0.84[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4287794	0.87[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4340549	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4371384	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4439990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4641969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4853510	0.98[ASN][1000 genomes]
rs4853710	0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4853713	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs4853716	0.98[ASN][1000 genomes]
rs56127319	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56342910	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58568707	0.89[EUR][1000 genomes]
rs59929070	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60915953	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61709084	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62180992	0.82[ASN][1000 genomes]
rs62181018	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62181019	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62181020	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62181029	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62181034	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62181052	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62182865	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62182885	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62182897	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6712426	0.98[ASN][1000 genomes]
rs6727669	0.98[ASN][1000 genomes]
rs6731287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7567059	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569128	0.86[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7581762	0.84[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7581986	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7593240	0.81[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12052514	HIBCH	cis	parietal	SCAN
rs12052514	INPP1	cis	cerebellum	SCAN
rs12052514	INPP1	cis	parietal	SCAN
rs12052514	INPP1	Cis_1M	lymphoblastoid	RTeQTL
rs12052514	MFSD6	cis	cerebellum	SCAN
rs12052514	HIBCH	cis	cerebellum	SCAN
rs12052514	MSTN	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191334800-191394800	Weak transcription	HSMMtube	muscle
2	chr2:191349600-191394600	Weak transcription	NHLF	lung
3	chr2:191351400-191385400	Weak transcription	NHEK	skin
4	chr2:191352200-191380600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:191352400-191381600	Weak transcription	Osteobl	bone
6	chr2:191354600-191394600	Weak transcription	HSMM	muscle
7	chr2:191357200-191398200	Weak transcription	Fetal Kidney	kidney
8	chr2:191358400-191379200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:191361600-191379800	Strong transcription	Fetal Thymus	thymus
10	chr2:191362200-191379200	Strong transcription	Dnd41	blood
11	chr2:191362800-191398200	Weak transcription	Fetal Brain Male	brain
12	chr2:191365000-191383200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:191365200-191380000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:191365200-191398000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:191365400-191392400	Weak transcription	HepG2	liver
16	chr2:191365800-191397400	Weak transcription	Liver	Liver
17	chr2:191366400-191386400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:191366600-191381000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:191367200-191393000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:191367400-191382400	Weak transcription	NHDF-Ad	bronchial
21	chr2:191368400-191379800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:191368600-191380000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:191369000-191379600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:191369000-191379800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:191369000-191394400	Weak transcription	Aorta	Aorta
26	chr2:191369200-191380000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:191370000-191380000	Weak transcription	Fetal Brain Female	brain
28	chr2:191370800-191382800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:191370800-191394400	Weak transcription	A549	lung
30	chr2:191371000-191379800	Weak transcription	Brain Germinal Matrix	brain
31	chr2:191371000-191393000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:191371800-191381000	Weak transcription	HMEC	breast
33	chr2:191372000-191394600	Weak transcription	Brain Anterior Caudate	brain
34	chr2:191372200-191378800	Weak transcription	Adipose Nuclei	Adipose
35	chr2:191372200-191385400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:191372200-191394600	Weak transcription	Brain Substantia Nigra	brain
37	chr2:191373800-191390800	Weak transcription	Spleen	Spleen
38	chr2:191374000-191378800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:191374000-191381200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:191374000-191384400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:191374000-191390800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:191374000-191390800	Weak transcription	Fetal Intestine Large	intestine
43	chr2:191374200-191378400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:191374200-191379800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:191374200-191380400	Weak transcription	Placenta	Placenta
46	chr2:191374400-191378200	Weak transcription	Fetal Lung	lung
47	chr2:191375200-191379400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:191375200-191382400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:191375200-191398600	Weak transcription	Ovary	ovary
50	chr2:191375400-191380000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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