Variant report

Variant	rs7745220
Chromosome Location	chr6:28919625-28919626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28863784..28865629-chr6:28918637..28921778,3	MCF-7	breast:
2	chr6:28807797..28809537-chr6:28919515..28922301,2	K562	blood:
3	chr6:28918185..28920512-chr6:28921430..28924835,3	MCF-7	breast:
4	chr6:28918865..28920559-chr6:28953984..28955919,2	MCF-7	breast:
5	chr6:28829833..28833248-chr6:28918976..28922184,3	K562	blood:
6	chr6:28916972..28925607-chr6:28947207..28951909,14	K562	blood:
7	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
8	chr6:28806197..28808344-chr6:28919521..28922266,2	MCF-7	breast:
9	chr6:28919130..28921907-chr6:28978530..28981244,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225173	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000244349	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000263426	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1041881	0.80[EUR][1000 genomes]
rs1056032	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12194037	0.92[EUR][1000 genomes]
rs17399888	0.85[EUR][1000 genomes]
rs2071786	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071787	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2071788	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28531681	0.88[EUR][1000 genomes]
rs2894065	0.89[EUR][1000 genomes]
rs3763338	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3763339	0.92[EUR][1000 genomes]
rs4713180	0.80[EUR][1000 genomes]
rs4713182	0.89[EUR][1000 genomes]
rs4713183	0.92[EUR][1000 genomes]
rs4713184	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4713191	0.95[EUR][1000 genomes]
rs4713195	0.86[EUR][1000 genomes]
rs4713196	0.89[EUR][1000 genomes]
rs4947256	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58958115	0.81[EUR][1000 genomes]
rs61751894	0.92[EUR][1000 genomes]
rs6928948	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6936343	0.86[EUR][1000 genomes]
rs72853516	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72853522	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72853523	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72860085	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72860099	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72862420	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72862423	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73741203	0.89[EUR][1000 genomes]
rs743848	0.86[EUR][1000 genomes]
rs7761745	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7762289	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295782	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9366731	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9366733	0.88[EUR][1000 genomes]
rs9380098	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380100	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380102	0.89[EUR][1000 genomes]
rs9380103	0.88[EUR][1000 genomes]
rs968723	0.95[EUR][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	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
2	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
3	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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28912200-28921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28912400-28920800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:28912400-28921200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:28912400-28921200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:28912400-28921200	Weak transcription	Right Atrium	heart
6	chr6:28915600-28921200	Weak transcription	Esophagus	oesophagus
7	chr6:28915800-28920600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:28916000-28920800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:28916000-28921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:28916200-28920800	Weak transcription	NH-A	brain
11	chr6:28916200-28920800	Weak transcription	Osteobl	bone
12	chr6:28916200-28921200	Weak transcription	HMEC	breast
13	chr6:28916200-28921200	Weak transcription	NHEK	skin
14	chr6:28916400-28921200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:28916600-28920600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:28916800-28921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:28917000-28920800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:28917000-28921200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:28918200-28919800	Active TSS	Placenta	Placenta
20	chr6:28918600-28921200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:28918800-28920800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:28918800-28920800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:28918800-28921000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:28919000-28921000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:28919200-28919800	Weak transcription	HepG2	liver
26	chr6:28919200-28920000	Enhancers	K562	blood
27	chr6:28919200-28920600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:28919200-28920800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:28919200-28920800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:28919200-28920800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:28919200-28921200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:28919400-28920200	Weak transcription	Hela-S3	cervix
33	chr6:28919600-28920200	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links