Variant report

Variant	rs4271171
Chromosome Location	chr1:178985658-178985659
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:

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10913677	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10913681	0.82[EUR][1000 genomes]
rs12041914	0.81[EUR][1000 genomes]
rs12725164	0.98[ASN][1000 genomes]
rs1408829	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766636	0.89[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4652343	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652350	0.85[CEU][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs4652352	0.85[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs6425514	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6699886	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517000	0.89[CEU][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs7517999	0.84[CEU][hapmap]
rs7526276	0.80[EUR][1000 genomes]
rs7541793	0.87[EUR][1000 genomes]
rs7548966	0.84[CEU][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs9729556	0.89[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][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	nsv548275	chr1:178978409-178985658	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4271171	TOR3A	cis	cerebellum	SCAN
rs4271171	FAM20B	cis	parietal	SCAN
rs4271171	ABL2	cis	parietal	SCAN
rs4271171	FAM20B	cis	lymphoblastoid	seeQTL
rs4271171	TOR3A	cis	Artery Tibial	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:178972400-178986000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:178978200-178986000	Weak transcription	HepG2	liver
3	chr1:178978600-178986000	Weak transcription	Right Atrium	heart
4	chr1:178978600-178991000	Weak transcription	Aorta	Aorta
5	chr1:178978600-178991200	Weak transcription	Psoas Muscle	Psoas
6	chr1:178981800-178986000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:178983800-178986000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:178984600-178986600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:178985000-178986000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:178985000-178986400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:178985000-178987200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:178985200-178986000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:178985200-178986600	Enhancers	Fetal Muscle Trunk	muscle
14	chr1:178985400-178986000	Enhancers	Duodenum Mucosa	Duodenum
15	chr1:178985400-178986000	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:178985400-178986000	Enhancers	A549	lung
17	chr1:178985400-178986000	Enhancers	Hela-S3	cervix
18	chr1:178985400-178986400	Enhancers	Colonic Mucosa	Colon
19	chr1:178985400-178986400	Enhancers	Stomach Mucosa	stomach
20	chr1:178985400-178987000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr1:178985400-178987200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr1:178985400-178987400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:178985400-178987400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:178985400-178988200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:178985400-178988200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:178985600-178985800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:178985600-178986000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:178985600-178986000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:178985600-178986000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:178985600-178986000	Enhancers	Brain Substantia Nigra	brain
31	chr1:178985600-178986000	Enhancers	HSMMtube	muscle
32	chr1:178985600-178986000	Enhancers	NHEK	skin
33	chr1:178985600-178986200	Enhancers	NHDF-Ad	bronchial
34	chr1:178985600-178986400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:178985600-178986400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:178985600-178986400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:178985600-178986400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:178985600-178986400	Enhancers	Adipose Nuclei	Adipose
39	chr1:178985600-178986400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr1:178985600-178986400	Enhancers	Esophagus	oesophagus
41	chr1:178985600-178986400	Enhancers	Fetal Intestine Large	intestine
42	chr1:178985600-178986400	Enhancers	Fetal Intestine Small	intestine
43	chr1:178985600-178986400	Enhancers	Fetal Stomach	stomach
44	chr1:178985600-178986400	Enhancers	Gastric	stomach
45	chr1:178985600-178986400	Enhancers	Lung	lung
46	chr1:178985600-178986400	Enhancers	Stomach Smooth Muscle	stomach
47	chr1:178985600-178986400	Enhancers	HSMM	muscle
48	chr1:178985600-178986400	Enhancers	NHLF	lung
49	chr1:178985600-178986600	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr1:178985600-178986600	Enhancers	Sigmoid Colon	Sigmoid Colon

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