Variant report

Variant	rs12520628
Chromosome Location	chr5:60702838-60702839
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60696992..60698821-chr5:60702298..60704382,2	MCF-7	breast:
2	chr5:60626312..60629944-chr5:60702524..60707105,7	MCF-7	breast:
3	chr5:60699528..60701144-chr5:60702112..60704567,2	MCF-7	breast:
4	chr5:60627607..60631817-chr5:60701781..60706248,8	MCF-7	breast:
5	chr5:60701139..60703224-chr5:60703240..60705056,2	MCF-7	breast:
6	chr5:60692035..60694385-chr5:60700898..60703629,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10041978	0.86[ASN][1000 genomes]
rs1045352	0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10939900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939901	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939902	0.99[ASN][1000 genomes]
rs10939903	0.86[ASN][1000 genomes]
rs10939905	0.80[ASN][1000 genomes]
rs11742658	0.80[ASN][1000 genomes]
rs11743711	0.88[ASN][1000 genomes]
rs11747564	0.80[ASN][1000 genomes]
rs11749200	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs11750589	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11950318	0.84[ASN][1000 genomes]
rs11952146	0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs11954430	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12187112	0.94[ASN][1000 genomes]
rs12188627	0.93[ASN][1000 genomes]
rs12189001	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518479	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522647	0.86[ASN][1000 genomes]
rs13156100	0.80[ASN][1000 genomes]
rs13157657	0.82[ASN][1000 genomes]
rs13157831	0.80[ASN][1000 genomes]
rs13158675	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13160801	0.82[ASN][1000 genomes]
rs13162358	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163970	0.82[ASN][1000 genomes]
rs13169711	1.00[ASN][1000 genomes]
rs13170135	0.98[ASN][1000 genomes]
rs13170262	0.82[ASN][1000 genomes]
rs13171497	0.80[ASN][1000 genomes]
rs13171757	0.88[ASN][1000 genomes]
rs13172080	0.82[ASN][1000 genomes]
rs13172084	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs13178686	0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179091	0.80[ASN][1000 genomes]
rs13181015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13185068	0.80[ASN][1000 genomes]
rs13186194	0.80[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs13188327	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13188685	0.80[ASN][1000 genomes]
rs1348716	0.82[ASN][1000 genomes]
rs1374043	0.82[ASN][1000 genomes]
rs1445976	0.80[ASN][1000 genomes]
rs1445979	0.86[ASN][1000 genomes]
rs1445980	0.80[ASN][1000 genomes]
rs1445981	0.80[ASN][1000 genomes]
rs1477355	0.86[ASN][1000 genomes]
rs1986252	0.82[ASN][1000 genomes]
rs2034239	0.80[ASN][1000 genomes]
rs2053693	0.80[ASN][1000 genomes]
rs2053694	0.80[ASN][1000 genomes]
rs2276987	0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs28610339	0.99[ASN][1000 genomes]
rs34739794	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35262187	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4276369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4392578	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484384	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604142	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5027472	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55838118	0.80[ASN][1000 genomes]
rs56035042	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60529601	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60886975	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62368660	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449527	0.81[CEU][hapmap]
rs6449528	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6449529	1.00[ASN][1000 genomes]
rs6449530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449531	0.99[ASN][1000 genomes]
rs6449532	0.99[ASN][1000 genomes]
rs6449533	0.99[ASN][1000 genomes]
rs6449535	0.86[ASN][1000 genomes]
rs66775554	0.80[ASN][1000 genomes]
rs6860608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6865624	0.80[ASN][1000 genomes]
rs6873712	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6874264	0.80[ASN][1000 genomes]
rs6877610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878927	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6879809	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6881765	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885005	0.99[ASN][1000 genomes]
rs6890351	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6894675	0.99[ASN][1000 genomes]
rs6895046	0.82[ASN][1000 genomes]
rs7443602	0.80[ASN][1000 genomes]
rs7700289	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7709645	0.99[ASN][1000 genomes]
rs7714457	0.82[ASN][1000 genomes]
rs7714712	0.99[ASN][1000 genomes]
rs7717082	0.82[ASN][1000 genomes]
rs7719647	0.82[ASN][1000 genomes]
rs7722810	0.87[ASN][1000 genomes]
rs7724551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7727824	0.99[ASN][1000 genomes]
rs7734879	0.99[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	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60659000-60703800	Weak transcription	Primary B cells from cord blood	blood
2	chr5:60659400-60703600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:60681200-60704000	Weak transcription	Brain Germinal Matrix	brain
4	chr5:60682000-60709800	Weak transcription	Left Ventricle	heart
5	chr5:60682600-60703600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:60682600-60704200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:60682600-60712400	Weak transcription	Esophagus	oesophagus
8	chr5:60685400-60704000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:60687400-60703600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:60687400-60705800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:60687600-60704400	Weak transcription	Ovary	ovary
12	chr5:60687600-60711800	Weak transcription	Aorta	Aorta
13	chr5:60687800-60703800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:60687800-60704200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:60690400-60703600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:60690800-60704400	Weak transcription	Psoas Muscle	Psoas
17	chr5:60690800-60705800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:60690800-60706800	Weak transcription	Gastric	stomach
19	chr5:60691000-60704400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:60694000-60703600	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:60694000-60705600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:60695200-60703600	Enhancers	A549	lung
23	chr5:60696600-60703600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:60697600-60703600	Weak transcription	HSMMtube	muscle
25	chr5:60697800-60703800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:60697800-60704400	Weak transcription	Pancreas	Pancrea
27	chr5:60698000-60703200	Weak transcription	HMEC	breast
28	chr5:60698000-60725400	Weak transcription	Spleen	Spleen
29	chr5:60698200-60703400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:60698200-60703400	Weak transcription	Fetal Heart	heart
31	chr5:60698200-60703600	Weak transcription	Osteobl	bone
32	chr5:60698200-60704000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:60698400-60703400	Weak transcription	NHEK	skin
34	chr5:60698400-60703600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:60698600-60703600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:60698600-60704000	Weak transcription	Primary T cells from cord blood	blood
37	chr5:60698800-60704000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:60699000-60703600	Weak transcription	NH-A	brain
39	chr5:60699400-60703200	Weak transcription	HSMM	muscle
40	chr5:60699400-60703400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:60699400-60703600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr5:60699400-60703600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:60699400-60703600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr5:60699400-60703600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr5:60699400-60703600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:60699400-60703600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:60699400-60703800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr5:60699400-60703800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:60699400-60703800	Weak transcription	Fetal Brain Female	brain
50	chr5:60699400-60704000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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