Variant report

Variant	rs2758873
Chromosome Location	chr6:39246856-39246857
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39246289..39249933-chr6:39249942..39252765,4	MCF-7	breast:
2	chr6:39135484..39137595-chr6:39246692..39248573,2	MCF-7	breast:
3	chr6:39236198..39237902-chr6:39244519..39247184,2	MCF-7	breast:
4	chr6:39243650..39250520-chr6:39262135..39271800,15	MCF-7	breast:
5	chr6:39246522..39249278-chr6:39249658..39251560,2	MCF-7	breast:
6	chr6:39242418..39244408-chr6:39246030..39248375,3	MCF-7	breast:
7	chr6:39245951..39248389-chr6:39255673..39257874,2	MCF-7	breast:
8	chr6:39245598..39248423-chr6:39251437..39253909,2	K562	blood:
9	chr6:39195286..39197963-chr6:39246502..39249488,3	K562	blood:
10	chr6:39191982..39197381-chr6:39245126..39249052,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11759627	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961538	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758870	0.94[EUR][1000 genomes]
rs2758879	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758880	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2758886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758896	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758905	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815033	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815034	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815043	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815047	1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815059	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815060	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815062	0.96[EUR][1000 genomes]
rs4711589	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55804343	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55812552	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55889689	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56011317	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56300329	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852940	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2758873	GLO1	cis	cerebellum	SCAN
rs2758873	LOC221442	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39240400-39250200	Enhancers	Stomach Mucosa	stomach
2	chr6:39242000-39247400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:39242000-39247800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:39242600-39247200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:39242600-39249600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:39243200-39247200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr6:39243600-39247000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:39243600-39247400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:39244400-39247600	Weak transcription	Pancreas	Pancrea
10	chr6:39244800-39247200	Weak transcription	Colonic Mucosa	Colon
11	chr6:39245600-39247200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:39245800-39248600	Enhancers	Placenta	Placenta
13	chr6:39246200-39251000	Enhancers	Liver	Liver
14	chr6:39246800-39247000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:39246800-39247000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
16	chr6:39246800-39248600	Enhancers	Small Intestine	intestine
17	chr6:39246800-39250400	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links