Variant report

Variant	rs6075068
Chromosome Location	chr20:16517950-16517951
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	chr20:16517798..16520614-chr20:16552938..16555340,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089177	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12479533	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12480324	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481403	0.90[AMR][1000 genomes]
rs17674942	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17743285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28763700	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6044078	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6044083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6044111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6044112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6044151	1.00[YRI][hapmap]
rs6075067	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6075069	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075076	0.90[AMR][1000 genomes]
rs6080285	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6080286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6080288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6080290	0.87[GIH][hapmap]
rs6080293	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6080295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080299	0.84[GIH][hapmap];0.86[TSI][hapmap]
rs6080301	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73101044	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73101048	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7352372	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs880800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6075068	HSPC072	cis	cerebellum	SCAN
rs6075068	KIF16B	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16485800-16521200	Weak transcription	Right Ventricle	heart
2	chr20:16489200-16521000	Weak transcription	Spleen	Spleen
3	chr20:16492600-16528800	Weak transcription	Primary B cells from cord blood	blood
4	chr20:16493000-16521200	Weak transcription	Liver	Liver
5	chr20:16497600-16521600	Weak transcription	Brain Hippocampus Middle	brain
6	chr20:16507400-16527000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr20:16508000-16522000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr20:16508400-16536800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr20:16509000-16522000	Weak transcription	Aorta	Aorta
10	chr20:16509200-16553000	Weak transcription	Primary T cells from cord blood	blood
11	chr20:16509600-16521600	Weak transcription	Fetal Muscle Leg	muscle
12	chr20:16511200-16518400	Weak transcription	NHEK	skin
13	chr20:16511400-16518600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr20:16511400-16519600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr20:16511400-16519800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr20:16511600-16522400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr20:16511600-16549000	Weak transcription	Colonic Mucosa	Colon
18	chr20:16511800-16518000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr20:16514400-16522000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr20:16516600-16520000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr20:16517400-16518200	Enhancers	Fetal Intestine Small	intestine
22	chr20:16517400-16518200	Enhancers	Left Ventricle	heart
23	chr20:16517400-16518200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr20:16517400-16518200	Enhancers	Small Intestine	intestine
25	chr20:16517400-16518400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr20:16517400-16518400	Enhancers	Fetal Intestine Large	intestine
27	chr20:16517400-16518400	Enhancers	Lung	lung
28	chr20:16517400-16518400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr20:16517400-16518600	Enhancers	Psoas Muscle	Psoas
30	chr20:16517400-16520200	Enhancers	Adipose Nuclei	Adipose
31	chr20:16517400-16521000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr20:16517600-16518000	Enhancers	Ovary	ovary
33	chr20:16517600-16518200	Enhancers	Duodenum Mucosa	Duodenum
34	chr20:16517600-16518200	Enhancers	HepG2	liver
35	chr20:16517600-16518400	Enhancers	Right Atrium	heart
36	chr20:16517600-16518600	Enhancers	Pancreas	Pancrea
37	chr20:16517600-16518800	Enhancers	Stomach Mucosa	stomach
38	chr20:16517800-16518200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr20:16517800-16518200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr20:16517800-16518200	Enhancers	Colon Smooth Muscle	Colon
41	chr20:16517800-16518400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr20:16517800-16521200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr20:16517800-16534200	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links