Variant report

Variant	rs1980379
Chromosome Location	chr6:144975518-144975519
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144968706..144970963-chr6:144974805..144976323,2	MCF-7	breast:
2	chr6:144971392..144973828-chr6:144974911..144976890,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10499232	0.91[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs11155364	0.91[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11155365	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11155370	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12209027	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12662483	0.87[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs12662875	0.85[ASN][1000 genomes]
rs17073972	0.87[JPT][hapmap]
rs17073995	0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs17074004	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2056744	0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2056745	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3950347	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4895646	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6907773	0.81[AMR][1000 genomes]
rs9373419	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs9373420	0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376835	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9376837	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9376838	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9386075	0.97[ASN][1000 genomes]
rs9386076	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9390184	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9390187	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390188	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9399483	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9399485	0.97[ASN][1000 genomes]
rs9399486	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399488	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9399489	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs9403572	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9403578	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv604822	chr6:144968195-145001887	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144949200-144980200	Weak transcription	Fetal Thymus	thymus
2	chr6:144951800-144977600	Weak transcription	Dnd41	blood
3	chr6:144961400-144978600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:144962800-144980200	Weak transcription	Ovary	ovary
5	chr6:144965600-144982400	Weak transcription	HSMM	muscle
6	chr6:144967000-144978600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:144967200-144982000	Weak transcription	HSMMtube	muscle
8	chr6:144967800-144980400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:144968200-144982000	Weak transcription	Brain Germinal Matrix	brain
10	chr6:144969400-144978800	Weak transcription	Pancreas	Pancrea
11	chr6:144970400-144976400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:144970600-144976200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:144970800-144975600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:144970800-144975800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:144971800-144978800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:144973000-144975800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr6:144973200-144975600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:144973200-144976600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:144973200-144976600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:144973200-144976800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:144973600-144975600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr6:144973600-144978800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:144973600-144980400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:144973600-144980400	Weak transcription	Colonic Mucosa	Colon
25	chr6:144974000-144980200	Weak transcription	Fetal Intestine Large	intestine
26	chr6:144974200-144976200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:144974200-144976600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:144974200-144977000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr6:144974400-144976000	Enhancers	Primary T cells fromperipheralblood	blood
30	chr6:144974600-144975600	Enhancers	Primary B cells from peripheral blood	blood
31	chr6:144974800-144975600	Flanking Active TSS	HepG2	liver
32	chr6:144974800-144978400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:144975000-144975600	Enhancers	Primary T cells from cord blood	blood
34	chr6:144975000-144975800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:144975000-144976000	Enhancers	Primary hematopoietic stem cells	blood
36	chr6:144975000-144976000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr6:144975000-144976600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr6:144975000-144976600	Enhancers	Liver	Liver
39	chr6:144975000-144976600	Enhancers	Fetal Lung	lung
40	chr6:144975000-144976600	Enhancers	NHDF-Ad	bronchial
41	chr6:144975000-144978800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr6:144975000-144978800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:144975200-144975600	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:144975200-144975600	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr6:144975200-144975600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr6:144975200-144975600	Enhancers	Small Intestine	intestine
47	chr6:144975200-144975800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr6:144975200-144975800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:144975200-144975800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:144975200-144975800	Enhancers	Fetal Intestine Small	intestine

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