Variant report

Variant	rs2439546
Chromosome Location	chr6:13313870-13313871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13311952..13314806-chr6:13320556..13323015,3	K562	blood:
2	chr6:13232923..13234560-chr6:13313162..13315905,2	K562	blood:
3	chr6:13271600..13273188-chr6:13312595..13314833,2	K562	blood:
4	chr6:13312615..13316148-chr6:13327198..13329955,3	MCF-7	breast:
5	chr6:13307272..13309683-chr6:13313078..13314603,2	K562	blood:

Variant related genes	Relation type
ENSG00000112137	Chromatin interaction
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12203576	0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1899262	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs202020	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439538	0.95[CEU][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2496141	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2496143	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2496155	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs364884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs381134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3846903	0.92[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs384730	0.82[JPT][hapmap]
rs408639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs408923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs412787	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs417048	0.82[JPT][hapmap]
rs442614	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs446843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs546520	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs570338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs629262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs629728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs641293	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs641688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6910418	0.82[AMR][1000 genomes]
rs7774863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9381915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9473896	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs9473901	0.86[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
3	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:13291800-13320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:13292000-13326000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:13292600-13326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:13298200-13326800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:13299600-13326600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:13299800-13326400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:13300200-13327000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:13301200-13325400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:13303400-13315200	Weak transcription	Small Intestine	intestine
13	chr6:13303400-13315800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:13303800-13315800	Weak transcription	HMEC	breast
15	chr6:13303800-13327800	Weak transcription	Stomach Mucosa	stomach
16	chr6:13304200-13315000	Weak transcription	Hela-S3	cervix
17	chr6:13304200-13315200	Weak transcription	Aorta	Aorta
18	chr6:13304400-13316800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:13304400-13327800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:13304600-13325600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:13304600-13326200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:13304800-13315200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:13304800-13315800	Weak transcription	Colonic Mucosa	Colon
24	chr6:13304800-13315800	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:13305200-13316400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:13305200-13325800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr6:13305400-13315800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:13305400-13315800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:13305400-13326200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr6:13305600-13315200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:13305800-13314800	Weak transcription	Esophagus	oesophagus
32	chr6:13305800-13315000	Weak transcription	NHLF	lung
33	chr6:13305800-13315200	Weak transcription	Lung	lung
34	chr6:13305800-13315200	Weak transcription	Pancreas	Pancrea
35	chr6:13305800-13315400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:13305800-13315800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:13305800-13316000	Weak transcription	Brain Angular Gyrus	brain
38	chr6:13305800-13319000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:13305800-13326200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:13306400-13314400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:13307200-13326200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr6:13307400-13326400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:13307800-13314400	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:13308000-13314400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:13308000-13315000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr6:13308000-13315200	Weak transcription	Spleen	Spleen
47	chr6:13308200-13316000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr6:13308600-13314000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:13308600-13315400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:13308600-13326400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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