Variant report

Variant	rs2271559
Chromosome Location	chr4:54362676-54362677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GSX2-4	chr4:54362567-54362766	ENSG00000250930.1

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10001201	0.95[CEU][hapmap]
rs10005424	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10007903	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10011259	0.81[CEU][hapmap]
rs10011394	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10028142	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10032903	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11133276	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11722866	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11723755	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11725230	0.95[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11734039	0.95[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11734681	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12507563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507739	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12508701	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651390	0.95[CEU][hapmap]
rs13150384	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1481819	0.81[CEU][hapmap]
rs1481824	0.81[CEU][hapmap]
rs1531748	0.85[CEU][hapmap]
rs17082893	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17082923	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17520800	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2090117	0.81[CEU][hapmap]
rs2271558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412447	0.82[CEU][hapmap]
rs2412488	0.81[CEU][hapmap]
rs28414913	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35089837	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35978987	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36011216	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3765158	0.81[CEU][hapmap]
rs3811785	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4864760	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4864767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57297394	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554104	1.00[CEU][hapmap]
rs6554105	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6554106	0.81[CEU][hapmap]
rs6818788	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6822201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825364	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6828559	0.90[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs6832626	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833766	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6838260	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6839922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840343	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843529	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7682199	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7686876	0.82[CEU][hapmap]
rs7688853	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7689981	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7690908	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7691578	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7691892	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698792	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs931181	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs931182	0.82[CEU][hapmap]
rs9312639	0.90[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs9995284	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9996883	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54329600-54373600	Weak transcription	Brain Germinal Matrix	brain
2	chr4:54329800-54374000	Weak transcription	Left Ventricle	heart
3	chr4:54333000-54363600	Weak transcription	Aorta	Aorta
4	chr4:54333000-54374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
6	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
7	chr4:54343400-54363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:54343600-54364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:54346400-54374000	Weak transcription	Right Ventricle	heart
10	chr4:54347600-54401800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:54355200-54378600	Weak transcription	Fetal Brain Male	brain
12	chr4:54356600-54373400	Weak transcription	Right Atrium	heart
13	chr4:54357400-54363000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:54357600-54362800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:54357800-54362800	Weak transcription	Fetal Lung	lung
16	chr4:54357800-54363000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:54357800-54363000	Weak transcription	Adipose Nuclei	Adipose
18	chr4:54357800-54363200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:54357800-54363400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:54357800-54363400	Weak transcription	Fetal Stomach	stomach
21	chr4:54357800-54363600	Weak transcription	NHDF-Ad	bronchial
22	chr4:54357800-54363600	Weak transcription	Osteobl	bone
23	chr4:54358600-54362800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:54358600-54365400	Weak transcription	Lung	lung
25	chr4:54359600-54363800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr4:54360000-54362800	Strong transcription	Liver	Liver
27	chr4:54360000-54363000	Strong transcription	Placenta	Placenta
28	chr4:54360600-54362800	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr4:54360600-54363600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:54361400-54364600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:54361800-54364000	Strong transcription	Fetal Intestine Small	intestine
32	chr4:54362000-54362800	Strong transcription	Brain Angular Gyrus	brain
33	chr4:54362000-54363200	Strong transcription	Esophagus	oesophagus
34	chr4:54362000-54363200	Strong transcription	Gastric	stomach
35	chr4:54362000-54363200	Strong transcription	Pancreas	Pancrea
36	chr4:54362000-54366600	Enhancers	Ovary	ovary
37	chr4:54362200-54362800	Enhancers	Fetal Muscle Trunk	muscle
38	chr4:54362200-54363000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:54362200-54363800	Strong transcription	Fetal Intestine Large	intestine
40	chr4:54362400-54363200	Strong transcription	HSMMtube	muscle
41	chr4:54362400-54374200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr4:54362600-54363000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:54362600-54363600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:54362600-54364600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:54362600-54368000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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