Variant report

Variant	rs2051772
Chromosome Location	chr11:17389850-17389851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17386801..17391541-chr11:17392806..17398479,7	K562	blood:
2	chr11:17373389..17376552-chr11:17389035..17393180,4	K562	blood:
3	chr11:17389738..17391541-chr11:17394315..17396637,3	K562	blood:

Variant related genes	Relation type
ENSG00000188211	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1002226	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10734252	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10832776	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024268	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024271	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12146443	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12146652	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1557765	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074311	0.84[CHB][hapmap]
rs2074314	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs4439492	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5213	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5215	0.88[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5219	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7124355	0.84[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap]
rs7484027	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs757110	0.88[ASW][hapmap];0.81[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs7928810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2051772	SERGEF	cis	parietal	SCAN
rs2051772	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs2051772	NCR3LG1	cis	Esophagus Mucosa	GTEx
rs2051772	SAA4	cis	parietal	SCAN
rs2051772	RP1-239B22.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17375400-17390200	Weak transcription	Small Intestine	intestine
2	chr11:17376000-17390000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr11:17376000-17391000	Weak transcription	Right Ventricle	heart
4	chr11:17376200-17390000	Weak transcription	Fetal Brain Male	brain
5	chr11:17376400-17390000	Weak transcription	HUVEC	blood vessel
6	chr11:17376400-17390600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr11:17376600-17391400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:17380200-17390200	Weak transcription	Osteobl	bone
9	chr11:17382400-17401200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:17385600-17390000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:17386200-17390000	Weak transcription	Brain Substantia Nigra	brain
12	chr11:17386800-17390000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr11:17386800-17390000	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr11:17386800-17390400	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr11:17387000-17390600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr11:17387200-17390400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:17387200-17398600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:17387400-17390000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr11:17387400-17391000	Strong transcription	Primary T cells from cord blood	blood
20	chr11:17387600-17390600	Enhancers	Placenta	Placenta
21	chr11:17387600-17393200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:17387800-17391200	Strong transcription	Pancreatic Islets	Pancreatic Islet
23	chr11:17388000-17390400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:17388000-17390600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:17388000-17391200	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr11:17388200-17391600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:17388200-17395200	ZNF genes & repeats	Thymus	Thymus
28	chr11:17388200-17395800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:17388200-17396800	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr11:17388400-17390000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:17388400-17390400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr11:17388400-17391600	Strong transcription	Gastric	stomach
33	chr11:17388400-17391800	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:17388600-17390000	Strong transcription	Left Ventricle	heart
35	chr11:17388600-17390000	Enhancers	HMEC	breast
36	chr11:17388600-17390200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:17388600-17390200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:17388600-17390400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:17388600-17391800	Strong transcription	Colon Smooth Muscle	Colon
40	chr11:17388600-17396000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
41	chr11:17388600-17396800	ZNF genes & repeats	Dnd41	blood
42	chr11:17388800-17390200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:17388800-17390600	Strong transcription	Brain Anterior Caudate	brain
44	chr11:17388800-17392000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
45	chr11:17388800-17392400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:17388800-17394200	ZNF genes & repeats	HepG2	liver
47	chr11:17388800-17395200	ZNF genes & repeats	Spleen	Spleen
48	chr11:17388800-17395600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
49	chr11:17388800-17395800	ZNF genes & repeats	HSMM	muscle
50	chr11:17388800-17395800	ZNF genes & repeats	NHEK	skin

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