Variant report

Variant	rs6080299
Chromosome Location	chr20:16526843-16526844
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:16525498..16527131-chr20:16552422..16555099,2	MCF-7	breast:
2	chr20:16525266..16528184-chr20:16551307..16555533,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089177	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10485553	1.00[JPT][hapmap]
rs10485555	1.00[JPT][hapmap]
rs12480660	1.00[JPT][hapmap]
rs12480678	1.00[JPT][hapmap]
rs1555195	1.00[JPT][hapmap]
rs17671618	1.00[JPT][hapmap]
rs17672161	1.00[JPT][hapmap]
rs17674942	0.84[GIH][hapmap]
rs1998085	1.00[JPT][hapmap]
rs2144896	1.00[JPT][hapmap]
rs6034498	1.00[JPT][hapmap]
rs6044009	1.00[JPT][hapmap]
rs6044021	1.00[JPT][hapmap]
rs6044111	0.82[CHB][hapmap]
rs6044112	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs6075068	0.84[GIH][hapmap];0.86[TSI][hapmap]
rs6075069	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs6075071	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6080286	0.84[GIH][hapmap]
rs6080290	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6080319	0.86[AMR][1000 genomes]
rs6080323	0.86[AMR][1000 genomes]
rs73101076	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73101078	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73102810	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73104828	0.94[AMR][1000 genomes]
rs73106807	0.94[AMR][1000 genomes]
rs73106829	0.83[AMR][1000 genomes]
rs7352087	0.86[AMR][1000 genomes]
rs8118656	1.00[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6080299	HSPC072	cis	cerebellum	SCAN
rs6080299	POLR3F	cis	cerebellum	SCAN
rs6080299	PHACTR2	trans	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16492600-16528800	Weak transcription	Primary B cells from cord blood	blood
2	chr20:16507400-16527000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr20:16508400-16536800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr20:16509200-16553000	Weak transcription	Primary T cells from cord blood	blood
5	chr20:16511600-16549000	Weak transcription	Colonic Mucosa	Colon
6	chr20:16517800-16534200	Weak transcription	Esophagus	oesophagus
7	chr20:16518200-16535800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr20:16518800-16534000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:16520200-16532000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr20:16520200-16534400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:16520400-16533800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr20:16520400-16534800	Weak transcription	Fetal Intestine Small	intestine
13	chr20:16522200-16533400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr20:16522600-16527800	Weak transcription	Brain Angular Gyrus	brain
15	chr20:16522600-16528200	Weak transcription	Lung	lung
16	chr20:16522800-16528400	Weak transcription	Spleen	Spleen
17	chr20:16522800-16532400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr20:16522800-16533800	Weak transcription	Right Ventricle	heart
19	chr20:16522800-16536800	Weak transcription	Aorta	Aorta
20	chr20:16523000-16533800	Weak transcription	Brain Anterior Caudate	brain
21	chr20:16523400-16528200	Weak transcription	Psoas Muscle	Psoas
22	chr20:16523400-16532600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr20:16523400-16535400	Weak transcription	Left Ventricle	heart
24	chr20:16523600-16528800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr20:16523800-16532400	Weak transcription	Ovary	ovary
26	chr20:16524000-16533800	Weak transcription	Small Intestine	intestine
27	chr20:16525000-16527800	Weak transcription	Pancreas	Pancrea
28	chr20:16525600-16532000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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