Variant report

Variant	rs11125098
Chromosome Location	chr2:47095007-47095008
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47085558..47087173-chr2:47093819..47096173,2	K562	blood:
2	chr2:46924424..46926689-chr2:47094250..47096324,2	K562	blood:
3	chr2:47088613..47092145-chr2:47092514..47095025,5	K562	blood:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13415138	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13422107	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278712	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34392693	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4953431	0.85[CEU][hapmap];0.94[MEX][hapmap]
rs4953434	0.85[CEU][hapmap];0.94[MEX][hapmap];0.84[AMR][1000 genomes]
rs58086358	0.91[EUR][1000 genomes]
rs61507430	0.84[EUR][1000 genomes]
rs7586009	1.00[JPT][hapmap]
rs875343	0.84[AMR][1000 genomes]
rs935380	0.84[AMR][1000 genomes]
rs9789584	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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11125098	MCFD2	cis	parietal	SCAN
rs11125098	MCFD2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47080800-47103600	Enhancers	Placenta	Placenta
2	chr2:47087800-47097400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:47089200-47096800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:47090000-47096200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:47091400-47096600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:47092000-47096400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:47092800-47095800	Enhancers	NHEK	skin
8	chr2:47093000-47095200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:47093000-47095200	Enhancers	Pancreas	Pancrea
10	chr2:47093000-47097800	Enhancers	Left Ventricle	heart
11	chr2:47093600-47095200	Enhancers	HUVEC	blood vessel
12	chr2:47093600-47096800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:47093600-47097000	Enhancers	Spleen	Spleen
14	chr2:47093800-47095600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:47093800-47098000	Enhancers	Right Ventricle	heart
16	chr2:47093800-47098200	Enhancers	Lung	lung
17	chr2:47094000-47095200	Enhancers	Stomach Mucosa	stomach
18	chr2:47094000-47095800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:47094000-47096400	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:47094000-47100600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:47094000-47104200	Weak transcription	Gastric	stomach
22	chr2:47094200-47096000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:47094200-47096200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:47094200-47096800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:47094200-47098200	Weak transcription	K562	blood
26	chr2:47094200-47100200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:47094200-47100400	Weak transcription	Colonic Mucosa	Colon
28	chr2:47094200-47100400	Weak transcription	Small Intestine	intestine
29	chr2:47094400-47095600	Weak transcription	Right Atrium	heart
30	chr2:47094400-47096200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:47094400-47096200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:47094400-47096800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:47094400-47101000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:47094600-47096600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:47094600-47100200	Weak transcription	Ovary	ovary
36	chr2:47094800-47095400	Enhancers	HMEC	breast
37	chr2:47094800-47097000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:47095000-47095200	Enhancers	Esophagus	oesophagus
39	chr2:47095000-47095600	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links