Variant report

Variant	rs6840343
Chromosome Location	chr4:54359680-54359681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54358927..54360648-chr4:54365691..54367691,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250930	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10001201	0.83[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs10005424	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10007903	0.86[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10011394	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10028142	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10032903	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11133276	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11722866	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11723755	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11725230	0.83[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11734039	0.83[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.84[TSI][hapmap]
rs11734681	0.87[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12507563	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507739	0.87[CEU][hapmap];0.91[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12508701	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511088	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511253	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642403	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649718	0.80[EUR][1000 genomes]
rs12651390	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs13150384	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17082893	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17082923	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17520800	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271558	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271559	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]
rs28414913	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35089837	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35978987	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36011216	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3811785	0.83[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4864760	0.83[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap]
rs4864767	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57297394	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554104	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs6554105	0.83[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs6818788	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6822201	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825364	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6828559	0.82[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs6832626	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833766	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6838260	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6839922	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840530	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843529	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7682199	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7686876	0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs7688853	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7689981	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7690908	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7691578	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7691892	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697622	0.80[EUR][1000 genomes]
rs7698792	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs931181	0.83[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs9312639	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs9995284	0.83[EUR][1000 genomes]
rs9996883	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54327800-54362200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:54328200-54362000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:54328400-54362000	Weak transcription	Brain Angular Gyrus	brain
4	chr4:54329600-54373600	Weak transcription	Brain Germinal Matrix	brain
5	chr4:54329800-54374000	Weak transcription	Left Ventricle	heart
6	chr4:54333000-54363600	Weak transcription	Aorta	Aorta
7	chr4:54333000-54374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:54342800-54360600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
10	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
11	chr4:54343400-54363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:54343600-54364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:54346400-54374000	Weak transcription	Right Ventricle	heart
14	chr4:54347600-54401800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:54348000-54362200	Weak transcription	Fetal Intestine Large	intestine
16	chr4:54349000-54360000	Weak transcription	Liver	Liver
17	chr4:54352800-54361800	Weak transcription	Fetal Intestine Small	intestine
18	chr4:54352800-54362000	Weak transcription	Esophagus	oesophagus
19	chr4:54353600-54362000	Weak transcription	Gastric	stomach
20	chr4:54353600-54362000	Weak transcription	Pancreas	Pancrea
21	chr4:54355200-54378600	Weak transcription	Fetal Brain Male	brain
22	chr4:54356600-54373400	Weak transcription	Right Atrium	heart
23	chr4:54356800-54362400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:54357200-54362600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:54357400-54363000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:54357600-54362200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:54357600-54362800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:54357800-54361800	Weak transcription	Stomach Mucosa	stomach
29	chr4:54357800-54362000	Weak transcription	Ovary	ovary
30	chr4:54357800-54362400	Weak transcription	HSMMtube	muscle
31	chr4:54357800-54362800	Weak transcription	Fetal Lung	lung
32	chr4:54357800-54363000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:54357800-54363000	Weak transcription	Adipose Nuclei	Adipose
34	chr4:54357800-54363200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:54357800-54363400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:54357800-54363400	Weak transcription	Fetal Stomach	stomach
37	chr4:54357800-54363600	Weak transcription	NHDF-Ad	bronchial
38	chr4:54357800-54363600	Weak transcription	Osteobl	bone
39	chr4:54358600-54362800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:54358600-54365400	Weak transcription	Lung	lung
41	chr4:54358800-54360000	Weak transcription	Placenta	Placenta
42	chr4:54359600-54363800	Strong transcription	Duodenum Mucosa	Duodenum

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