Variant report

Variant	rs6546032
Chromosome Location	chr2:64075076-64075077
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64066407..64070482-chr2:64071096..64075382,10	MCF-7	breast:
2	chr2:64071888..64074262-chr2:64074746..64076880,2	MCF-7	breast:
3	chr2:64074326..64076257-chr2:64078253..64080892,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10183479	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11558741	1.00[ASN][1000 genomes]
rs11674020	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676710	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11683408	0.92[ASN][1000 genomes]
rs11686956	0.82[ASN][1000 genomes]
rs11691987	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11693906	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11694253	0.83[ASN][1000 genomes]
rs11695421	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713498	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12996866	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13018690	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13431781	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440002	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17562177	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17562423	0.90[ASN][1000 genomes]
rs17619753	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs193031	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2302808	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2969395	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs329478	0.88[ASN][1000 genomes]
rs329488	0.80[ASN][1000 genomes]
rs34122334	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34765999	0.88[ASN][1000 genomes]
rs34777730	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs35002211	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35336851	0.83[ASN][1000 genomes]
rs35474183	0.88[ASN][1000 genomes]
rs35480874	0.88[ASN][1000 genomes]
rs35697586	0.88[ASN][1000 genomes]
rs35960986	0.82[ASN][1000 genomes]
rs36033991	0.98[ASN][1000 genomes]
rs36123537	0.90[ASN][1000 genomes]
rs4233930	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4538187	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671071	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671073	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56904032	0.92[ASN][1000 genomes]
rs6546029	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546030	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546033	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546035	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66980330	1.00[ASN][1000 genomes]
rs6710763	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6715992	0.91[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67308158	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731508	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732746	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755646	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67615384	0.96[ASN][1000 genomes]
rs67765474	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68117986	0.92[ASN][1000 genomes]
rs72808243	0.96[ASN][1000 genomes]
rs72893103	0.92[ASN][1000 genomes]
rs7590399	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64067000-64075800	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:64067000-64076400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:64070000-64082800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:64070200-64076400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:64070200-64084600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:64070200-64103000	Weak transcription	Gastric	stomach
7	chr2:64070400-64075800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:64070600-64076600	Enhancers	Brain Substantia Nigra	brain
9	chr2:64070600-64082800	Weak transcription	Fetal Stomach	stomach
10	chr2:64070600-64083800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:64070800-64075800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:64070800-64076000	Enhancers	Brain Hippocampus Middle	brain
13	chr2:64070800-64082600	Weak transcription	HUVEC	blood vessel
14	chr2:64071000-64076200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:64071200-64076000	Weak transcription	Fetal Kidney	kidney
16	chr2:64071200-64076200	Weak transcription	Fetal Lung	lung
17	chr2:64071200-64076400	Weak transcription	Fetal Brain Male	brain
18	chr2:64071200-64080600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:64071600-64076400	Weak transcription	Stomach Mucosa	stomach
20	chr2:64071800-64076600	Weak transcription	Fetal Intestine Large	intestine
21	chr2:64071800-64076800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:64071800-64080200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr2:64071800-64080600	Weak transcription	Pancreas	Pancrea
24	chr2:64072000-64076000	Weak transcription	NH-A	brain
25	chr2:64072000-64076200	Weak transcription	Fetal Brain Female	brain
26	chr2:64072000-64076600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:64072000-64076600	Weak transcription	K562	blood
28	chr2:64072000-64080600	Weak transcription	Lung	lung
29	chr2:64072000-64081200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:64072000-64082800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:64072000-64082800	Weak transcription	Placenta	Placenta
32	chr2:64072000-64084200	Weak transcription	Esophagus	oesophagus
33	chr2:64072200-64076800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:64072200-64076800	Weak transcription	Fetal Thymus	thymus
35	chr2:64072200-64079600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr2:64072400-64075200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:64072400-64075400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
38	chr2:64072600-64075800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:64072600-64076000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:64072600-64076800	Weak transcription	Primary T cells from cord blood	blood
41	chr2:64072600-64084600	Weak transcription	Hela-S3	cervix
42	chr2:64073000-64076000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:64073000-64076600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:64073000-64081800	Weak transcription	Colonic Mucosa	Colon
45	chr2:64073000-64083200	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:64073200-64076400	Weak transcription	HMEC	breast
47	chr2:64073200-64076600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:64073200-64076600	Enhancers	HepG2	liver
49	chr2:64073200-64078400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:64073400-64075800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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