Variant report

Variant	rs2050159
Chromosome Location	chr6:53773153-53773154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53768489..53771106-chr6:53771711..53773800,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10456168	0.82[EUR][1000 genomes]
rs10755768	0.88[EUR][1000 genomes]
rs12661938	0.83[ASN][1000 genomes]
rs12663216	0.95[JPT][hapmap]
rs1543356	1.00[YRI][hapmap]
rs2006013	0.80[EUR][1000 genomes]
rs3003492	0.94[JPT][hapmap]
rs3003498	0.94[JPT][hapmap]
rs34299171	0.80[EUR][1000 genomes]
rs35081045	0.84[EUR][1000 genomes]
rs4273680	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4478409	0.87[JPT][hapmap]
rs4486000	0.94[JPT][hapmap]
rs4582388	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4715428	0.84[EUR][1000 genomes]
rs4715429	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62397090	0.88[ASN][1000 genomes]
rs6458973	0.89[EUR][1000 genomes]
rs6902746	0.80[EUR][1000 genomes]
rs6905323	0.83[ASN][1000 genomes]
rs6905563	0.88[JPT][hapmap]
rs6906326	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6907354	0.89[EUR][1000 genomes]
rs6916929	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6925391	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6935942	0.82[EUR][1000 genomes]
rs761135	0.86[YRI][hapmap]
rs7744962	0.80[EUR][1000 genomes]
rs7750173	0.90[ASN][1000 genomes]
rs7769351	0.80[EUR][1000 genomes]
rs7773779	0.80[EUR][1000 genomes]
rs9357777	0.87[EUR][1000 genomes]
rs9370245	0.88[EUR][1000 genomes]
rs9395890	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs9395891	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs9463988	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9463996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9463997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474643	0.83[JPT][hapmap]
rs9474671	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9474680	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:53754800-53775600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:53754800-53779800	Weak transcription	NHLF	lung
4	chr6:53755000-53779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:53756000-53781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:53758000-53775600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
8	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
9	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
12	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
13	chr6:53760600-53778800	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:53761000-53782000	Weak transcription	Fetal Kidney	kidney
16	chr6:53761000-53782800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:53761000-53785400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:53761400-53776400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:53761400-53787400	Weak transcription	HMEC	breast
20	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
22	chr6:53761800-53777000	Strong transcription	Fetal Thymus	thymus
23	chr6:53761800-53786800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:53762000-53774000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr6:53762000-53775600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
28	chr6:53762200-53786800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:53762800-53775600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:53764400-53784600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:53768000-53774600	Weak transcription	HUVEC	blood vessel
32	chr6:53768600-53785000	Weak transcription	Primary B cells from cord blood	blood
33	chr6:53768800-53775600	Weak transcription	Brain Germinal Matrix	brain
34	chr6:53768800-53778600	Weak transcription	Aorta	Aorta
35	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:53769000-53785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:53769200-53777000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:53769200-53778600	Weak transcription	Esophagus	oesophagus
39	chr6:53769200-53790400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr6:53769400-53777600	Weak transcription	Small Intestine	intestine
41	chr6:53769600-53785200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:53769800-53779000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:53769800-53784400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:53769800-53784400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:53770000-53778600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:53770000-53778600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:53770000-53781800	Weak transcription	HSMM	muscle
48	chr6:53770000-53782000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:53770400-53778800	Weak transcription	Fetal Muscle Trunk	muscle

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