Variant report

Variant	rs3862794
Chromosome Location	chr11:72538600-72538601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:72534107..72536304-chr11:72538000..72539658,2	K562	blood:
2	chr11:72536642..72539499-chr11:72952238..72954950,2	K562	blood:
3	chr11:72529288..72531257-chr11:72537925..72540792,2	K562	blood:
4	chr11:72531953..72533844-chr11:72537907..72539581,2	K562	blood:

Variant related genes	Relation type
ENSG00000168010	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10793048	0.85[MEX][hapmap];0.83[AMR][1000 genomes]
rs10898885	0.85[MEX][hapmap];0.80[AMR][1000 genomes]
rs10898889	0.82[AMR][1000 genomes]
rs11822039	0.92[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs12799445	0.83[AMR][1000 genomes]
rs12805658	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12808517	0.84[CEU][hapmap]
rs3862796	0.92[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs4400839	0.86[GIH][hapmap]
rs4944014	0.89[AMR][1000 genomes]
rs4944016	0.91[CEU][hapmap]
rs593753	0.92[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs6592500	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6592505	0.84[CEU][hapmap]
rs7946861	0.84[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
2	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3862794	FCHSD2	cis	parietal	SCAN
rs3862794	PDE2A	cis	parietal	SCAN
rs3862794	STARD10	cis	cerebellum	SCAN
rs3862794	ATG16L2	cis	parietal	SCAN
rs3862794	STARD10	cis	Whole Blood	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72528800-72542800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr11:72529000-72543600	Strong transcription	Dnd41	blood
3	chr11:72532600-72542400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr11:72533000-72538600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:72533200-72541400	Weak transcription	HSMMtube	muscle
6	chr11:72533600-72539000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:72533600-72539000	Weak transcription	Liver	Liver
8	chr11:72533600-72539200	Weak transcription	Left Ventricle	heart
9	chr11:72533600-72539200	Weak transcription	Ovary	ovary
10	chr11:72533600-72539400	Weak transcription	Gastric	stomach
11	chr11:72533600-72542200	Weak transcription	NHEK	skin
12	chr11:72533600-72542400	Weak transcription	Fetal Lung	lung
13	chr11:72533600-72542600	Weak transcription	Stomach Mucosa	stomach
14	chr11:72533600-72542800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:72533600-72542800	Weak transcription	Hela-S3	cervix
16	chr11:72533800-72538800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:72533800-72538800	Weak transcription	Adipose Nuclei	Adipose
18	chr11:72533800-72538800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:72533800-72539000	Weak transcription	NHLF	lung
20	chr11:72533800-72539200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:72533800-72539200	Weak transcription	Colonic Mucosa	Colon
22	chr11:72533800-72539200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr11:72533800-72539400	Weak transcription	Aorta	Aorta
24	chr11:72533800-72539400	Weak transcription	Pancreas	Pancrea
25	chr11:72533800-72539600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:72533800-72539600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:72533800-72541000	Strong transcription	Primary hematopoietic stem cells	blood
28	chr11:72533800-72542000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:72533800-72542400	Weak transcription	Brain Angular Gyrus	brain
30	chr11:72533800-72542600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:72533800-72542600	Weak transcription	Brain Substantia Nigra	brain
32	chr11:72533800-72542600	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:72533800-72542600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:72533800-72542600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr11:72533800-72542600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr11:72533800-72542600	Weak transcription	HMEC	breast
37	chr11:72533800-72549400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr11:72534000-72538600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr11:72534000-72539000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr11:72534000-72539000	Weak transcription	Osteobl	bone
41	chr11:72534000-72539400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:72534000-72539400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:72534000-72539400	Weak transcription	Brain Germinal Matrix	brain
44	chr11:72534000-72539600	Weak transcription	Brain Anterior Caudate	brain
45	chr11:72534000-72540200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:72534000-72541000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:72534000-72541800	Strong transcription	Thymus	Thymus
48	chr11:72534000-72542000	Strong transcription	Esophagus	oesophagus
49	chr11:72534000-72542400	Weak transcription	Brain Hippocampus Middle	brain
50	chr11:72534000-72542600	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links