Variant report

Variant	rs12567630
Chromosome Location	chr1:178986624-178986625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:178977019..178978702-chr1:178984062..178987860,3	K562	blood:
2	chr1:178978287..178981942-chr1:178982197..178988679,6	K562	blood:
3	chr1:178984886..178987264-chr1:179011722..179014379,2	K562	blood:
4	chr1:178985118..178988730-chr1:179014832..179016869,4	K562	blood:
5	chr1:178985568..178988566-chr1:179021410..179023796,2	K562	blood:
6	chr1:178982170..178984787-chr1:178986294..178987843,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10913673	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913676	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10913681	0.91[ASN][1000 genomes]
rs10913689	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs12064702	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12568291	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12725164	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12733622	0.93[CHD][hapmap];0.84[JPT][hapmap]
rs12735672	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2025581	0.86[ASN][1000 genomes]
rs2209453	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2224962	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2224963	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274227	0.82[EUR][1000 genomes]
rs34636548	0.89[ASN][1000 genomes]
rs3766636	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4651011	0.91[ASN][1000 genomes]
rs4652346	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4652349	0.91[ASN][1000 genomes]
rs4652350	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs4652352	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs4652353	0.86[ASN][1000 genomes]
rs4652355	0.85[CEU][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs6425516	0.91[ASN][1000 genomes]
rs67498652	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7517000	0.87[CHB][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap]
rs7517999	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7520456	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7526276	0.89[ASN][1000 genomes]
rs7541378	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541793	0.96[ASN][1000 genomes]
rs7548966	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs9729556	0.87[CHB][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12567630	FAM20B	cis	lymphoblastoid	seeQTL
rs12567630	ABL2	cis	parietal	SCAN
rs12567630	TOR3A	cis	Artery Tibial	GTEx
rs12567630	FAM20B	cis	parietal	SCAN
rs12567630	TOR3A	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:178978600-178991000	Weak transcription	Aorta	Aorta
2	chr1:178978600-178991200	Weak transcription	Psoas Muscle	Psoas
3	chr1:178985000-178987200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:178985400-178987000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr1:178985400-178987200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:178985400-178987400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr1:178985400-178987400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:178985400-178988200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:178985400-178988200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:178985600-178987000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:178985600-178987400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:178985600-178987400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:178985600-178987400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:178985600-178987400	Enhancers	Left Ventricle	heart
15	chr1:178985600-178987400	Enhancers	HMEC	breast
16	chr1:178985600-178987600	Enhancers	Fetal Muscle Leg	muscle
17	chr1:178985600-178987600	Enhancers	Ovary	ovary
18	chr1:178985600-178987600	Flanking Active TSS	K562	blood
19	chr1:178985600-178988600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:178985800-178987400	Enhancers	Brain Angular Gyrus	brain
21	chr1:178985800-178987400	Enhancers	Fetal Heart	heart
22	chr1:178986000-178986800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:178986000-178986800	Enhancers	Liver	Liver
24	chr1:178986000-178986800	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr1:178986000-178986800	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr1:178986000-178986800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:178986000-178987000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:178986000-178987000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:178986000-178987000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:178986000-178987200	Enhancers	Colon Smooth Muscle	Colon
31	chr1:178986000-178987200	Enhancers	Fetal Lung	lung
32	chr1:178986000-178987200	Flanking Active TSS	HepG2	liver
33	chr1:178986000-178987400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:178986000-178987400	Enhancers	Brain Cingulate Gyrus	brain
35	chr1:178986000-178987400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:178986000-178987400	Flanking Active TSS	A549	lung
37	chr1:178986000-178987400	Flanking Active TSS	Hela-S3	cervix
38	chr1:178986000-178987400	Enhancers	NH-A	brain
39	chr1:178986000-178987400	Enhancers	Osteobl	bone
40	chr1:178986000-178987800	Enhancers	Placenta	Placenta
41	chr1:178986200-178986800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:178986200-178987400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:178986200-178987400	Flanking Active TSS	NHDF-Ad	bronchial
44	chr1:178986400-178986800	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr1:178986400-178986800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr1:178986400-178986800	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr1:178986400-178986800	Flanking Active TSS	HSMM	muscle
48	chr1:178986400-178986800	Flanking Active TSS	NHLF	lung
49	chr1:178986400-178987000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:178986400-178987000	Flanking Active TSS	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links