Variant report

Variant	rs638492
Chromosome Location	chr11:86217761-86217762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86216870..86219202-chr11:86219974..86222344,3	MCF-7	breast:
2	chr11:86216398..86218909-chr11:86219369..86221994,2	MCF-7	breast:
3	chr11:86209007..86213257-chr11:86214402..86217929,5	MCF-7	breast:
4	chr11:86209967..86211893-chr11:86216678..86219275,2	K562	blood:

Variant related genes	Relation type
ENSG00000151376	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10751139	0.84[ASN][1000 genomes]
rs11234691	0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2446224	0.85[CHB][hapmap]
rs2446225	0.90[CHB][hapmap]
rs2446230	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[ASN][1000 genomes]
rs2511082	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs2511083	0.82[ASN][1000 genomes]
rs4944588	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs579719	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs582282	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs583594	0.90[CHB][hapmap]
rs584953	0.90[CHB][hapmap]
rs587362	0.91[ASN][1000 genomes]
rs590750	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs601646	0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs610790	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[ASN][1000 genomes]
rs611730	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[ASN][1000 genomes]
rs614995	0.90[CHB][hapmap];0.95[CHD][hapmap];0.80[ASN][1000 genomes]
rs616794	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs620054	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs630454	0.89[ASN][1000 genomes]
rs631082	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs632873	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs633708	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs641541	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs643414	0.94[ASN][1000 genomes]
rs647561	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs651758	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs653715	0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs658324	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs660372	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[ASN][1000 genomes]
rs661163	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs661328	0.81[ASN][1000 genomes]
rs663208	0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.90[ASN][1000 genomes]
rs664613	0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.80[LWK][hapmap];0.91[ASN][1000 genomes]
rs669325	0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.91[ASN][1000 genomes]
rs675775	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs676106	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs677301	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs677643	0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs679977	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs681333	0.91[ASN][1000 genomes]
rs683899	0.86[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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv898056	chr11:86156848-86304402	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs638492	PRSS23	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86160200-86221000	Weak transcription	Primary T cells from cord blood	blood
2	chr11:86172400-86227000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:86187600-86218600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:86189200-86222600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:86189600-86221600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:86195200-86222200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:86198600-86222800	Weak transcription	Esophagus	oesophagus
8	chr11:86202800-86226400	Weak transcription	Fetal Lung	lung
9	chr11:86204000-86222200	Weak transcription	Colon Smooth Muscle	Colon
10	chr11:86204600-86220000	Weak transcription	Colonic Mucosa	Colon
11	chr11:86209200-86218800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:86209200-86219600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:86209200-86221200	Weak transcription	NH-A	brain
14	chr11:86209200-86223600	Weak transcription	Brain Angular Gyrus	brain
15	chr11:86209200-86226600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr11:86209400-86219200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:86209400-86220000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:86209400-86221600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:86209400-86221600	Weak transcription	HSMM	muscle
20	chr11:86209600-86218400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:86209600-86221800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:86209800-86218200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:86211400-86218200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr11:86211400-86222800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:86211600-86220000	Weak transcription	Pancreas	Pancrea
26	chr11:86211600-86229800	Weak transcription	Brain Anterior Caudate	brain
27	chr11:86211800-86219400	Weak transcription	Fetal Heart	heart
28	chr11:86212000-86220200	Weak transcription	Right Atrium	heart
29	chr11:86212800-86221600	Weak transcription	K562	blood
30	chr11:86213000-86218400	Weak transcription	Stomach Mucosa	stomach
31	chr11:86213800-86219200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:86214800-86222000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:86215000-86229800	Weak transcription	Lung	lung
34	chr11:86215200-86221800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:86215200-86222400	Weak transcription	Ovary	ovary
36	chr11:86215200-86222600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr11:86215200-86223400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr11:86215200-86226400	Weak transcription	Spleen	Spleen
39	chr11:86215400-86219000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:86215400-86219200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:86215400-86219200	Weak transcription	HMEC	breast
42	chr11:86215400-86219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:86215400-86219400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:86215400-86219400	Weak transcription	HUVEC	blood vessel
45	chr11:86215400-86219400	Weak transcription	Osteobl	bone
46	chr11:86215400-86219800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:86215400-86220000	Weak transcription	HSMMtube	muscle
48	chr11:86215400-86221000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:86215400-86222400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:86215400-86222400	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links