Variant report

Variant	rs7762289
Chromosome Location	chr6:28910235-28910236
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr6:28910215-28910353	MCF10A-Er-Src	breast:	n/a	n/a
2	KAP1	chr6:28908146-28910242	U2OS	brain:	n/a	n/a
3	SREBP2	chr6:28907038-28910590	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
2	chr6:28745229..28748097-chr6:28908724..28910861,2	K562	blood:
3	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
4	chr6:28908321..28911202-chr6:103515957..103517476,2	K562	blood:
5	chr6:28806425..28808572-chr6:28907026..28910761,3	K562	blood:
6	chr6:28909868..28911383-chr6:28971101..28973508,2	K562	blood:
7	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
8	chr6:28907996..28910654-chr6:28948439..28951310,2	MCF-7	breast:
9	chr6:28803772..28808857-chr6:28906937..28913057,11	K562	blood:
10	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
11	chr6:27775703..27777987-chr6:28908653..28911644,2	K562	blood:

No data

Variant related genes	Relation type
C6orf100	TF binding region
ENSG00000196747	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000263426	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1056032	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12194037	0.88[EUR][1000 genomes]
rs2071786	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2071787	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2071788	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3763338	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3763339	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713183	0.82[EUR][1000 genomes]
rs4713184	0.91[EUR][1000 genomes]
rs4713191	0.83[EUR][1000 genomes]
rs4947256	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58958115	0.88[EUR][1000 genomes]
rs6928948	0.83[ASN][1000 genomes]
rs72853516	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72853522	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72853523	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72860085	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72860099	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72862420	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72862423	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7745220	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7761745	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295782	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9366731	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380098	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380100	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380102	0.82[EUR][1000 genomes]
rs968723	0.83[EUR][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	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28906600-28912600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:28907400-28912400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:28907400-28912400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:28907400-28912400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr6:28907400-28912400	Active TSS	A549	lung
6	chr6:28907400-28912800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:28907400-28913400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:28907800-28912400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:28907800-28912400	Active TSS	Rectal Smooth Muscle	rectum
10	chr6:28909400-28911200	Weak transcription	Small Intestine	intestine
11	chr6:28909400-28911200	Weak transcription	Spleen	Spleen
12	chr6:28909400-28911400	Weak transcription	Gastric	stomach
13	chr6:28909400-28911400	Weak transcription	Lung	lung
14	chr6:28909600-28910400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:28909600-28911000	Weak transcription	Esophagus	oesophagus
16	chr6:28909600-28911200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:28909600-28911400	Weak transcription	Aorta	Aorta
18	chr6:28909600-28911400	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr6:28909800-28910400	Enhancers	Liver	Liver
20	chr6:28909800-28910400	Enhancers	Fetal Heart	heart
21	chr6:28909800-28910400	Enhancers	Placenta	Placenta
22	chr6:28909800-28910400	Flanking Active TSS	Hela-S3	cervix
23	chr6:28909800-28911000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:28909800-28911200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr6:28909800-28911600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:28910000-28910400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr6:28910000-28910400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:28910000-28910400	Bivalent/Poised TSS	Fetal Brain Female	brain
29	chr6:28910000-28910400	Enhancers	Fetal Kidney	kidney
30	chr6:28910000-28910400	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr6:28910000-28910400	Bivalent Enhancer	Fetal Thymus	thymus
32	chr6:28910000-28911000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:28910000-28911000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:28910000-28911000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:28910000-28911000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr6:28910000-28911000	Enhancers	Primary T cells from cord blood	blood
37	chr6:28910000-28911000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr6:28910000-28911000	Weak transcription	HUVEC	blood vessel
39	chr6:28910000-28911200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr6:28910000-28911200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:28910000-28911200	Enhancers	Primary B cells from peripheral blood	blood
42	chr6:28910000-28911200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr6:28910000-28911200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:28910000-28911200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:28910000-28911200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:28910000-28911200	Weak transcription	Left Ventricle	heart
47	chr6:28910000-28911200	Weak transcription	Pancreas	Pancrea
48	chr6:28910000-28911200	Weak transcription	Right Atrium	heart
49	chr6:28910000-28911200	Flanking Active TSS	K562	blood
50	chr6:28910000-28911400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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