Variant report

Variant	rs11962883
Chromosome Location	chr6:133118491-133118492
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr6:133118194-133118507	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133117688..133126502-chr6:133133829..133139054,19	MCF-7	breast:

Variant related genes	Relation type
SLC18B1	TF binding region
ENSG00000221500	Chromatin interaction
ENSG00000112306	Chromatin interaction
ENSG00000206754	Chromatin interaction
ENSG00000200534	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10457596	0.88[ASN][1000 genomes]
rs10484629	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964512	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12198849	0.88[ASN][1000 genomes]
rs12203977	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12204027	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12211701	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1467403	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1467404	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813347	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58832890	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61421874	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62424539	0.88[ASN][1000 genomes]
rs6569847	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6569848	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6910639	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6912936	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6915168	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6934161	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73554431	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7738071	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7758703	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7761365	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7765224	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7769051	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7770081	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9321367	0.94[ASN][1000 genomes]
rs9321371	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9399041	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493435	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493437	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493438	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493443	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9493444	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9493445	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9493446	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9493454	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv886676	chr6:133111706-133168582	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133085000-133119000	Weak transcription	Thymus	Thymus
2	chr6:133085200-133119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:133085600-133118800	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:133085800-133119000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:133086000-133118800	Weak transcription	Fetal Kidney	kidney
6	chr6:133089400-133119400	Weak transcription	Gastric	stomach
7	chr6:133089600-133118800	Weak transcription	Fetal Heart	heart
8	chr6:133089600-133119000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:133089600-133119200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:133089600-133119200	Weak transcription	Right Ventricle	heart
11	chr6:133089600-133119200	Weak transcription	Stomach Mucosa	stomach
12	chr6:133089600-133119400	Weak transcription	Pancreas	Pancrea
13	chr6:133089800-133118800	Weak transcription	Brain Angular Gyrus	brain
14	chr6:133090000-133118800	Weak transcription	HepG2	liver
15	chr6:133091800-133119000	Weak transcription	Psoas Muscle	Psoas
16	chr6:133098400-133119000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:133098400-133119000	Weak transcription	Brain Substantia Nigra	brain
18	chr6:133098600-133118800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:133100400-133118600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:133100400-133118800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:133100400-133119000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:133100600-133118800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:133100600-133118800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:133100600-133118800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:133100600-133119000	Weak transcription	Aorta	Aorta
26	chr6:133100600-133119000	Weak transcription	Fetal Thymus	thymus
27	chr6:133100600-133119000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:133101000-133118800	Weak transcription	Liver	Liver
29	chr6:133103000-133119000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr6:133106600-133119200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:133108600-133119200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:133108800-133118800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:133109200-133118800	Weak transcription	A549	lung
34	chr6:133110600-133118800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:133110600-133119000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:133110800-133118800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:133110800-133119000	Weak transcription	Colonic Mucosa	Colon
38	chr6:133110800-133119200	Weak transcription	Esophagus	oesophagus
39	chr6:133110800-133119200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:133111200-133118600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:133111400-133119000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:133111800-133118600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:133112800-133118800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:133113000-133118600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr6:133113000-133118800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:133113000-133118800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:133113200-133118800	Weak transcription	HUVEC	blood vessel
48	chr6:133114000-133118800	Weak transcription	HMEC	breast
49	chr6:133114200-133118800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr6:133114800-133118600	Weak transcription	Primary T cells from cord blood	blood

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