Variant report

Variant	rs1326947
Chromosome Location	chr11:35024965-35024966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1117051	0.87[JPT][hapmap]
rs1326944	0.80[AMR][1000 genomes]
rs1359725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1409716	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1553760	0.81[CHD][hapmap]
rs1960524	0.88[JPT][hapmap];0.80[AMR][1000 genomes]
rs1991648	0.88[JPT][hapmap]
rs2031686	0.85[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs2147341	0.80[AMR][1000 genomes]
rs2732556	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2761823	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2767037	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915187	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915189	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2915191	0.94[ASN][1000 genomes]
rs2915198	0.88[JPT][hapmap]
rs2915214	0.85[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs2915217	0.85[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs2915218	0.80[AMR][1000 genomes]
rs2915225	0.88[JPT][hapmap]
rs2956077	0.93[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2956086	0.88[JPT][hapmap]
rs2956095	0.88[JPT][hapmap]
rs2956097	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs2956098	0.92[JPT][hapmap]
rs2956116	0.85[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs2956118	0.81[CEU][hapmap]
rs2956120	0.80[AMR][1000 genomes]
rs2956125	0.88[JPT][hapmap]
rs2985150	0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2985382	0.88[JPT][hapmap]
rs2985385	0.80[AMR][1000 genomes]
rs2986402	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986403	0.93[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2986405	0.93[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2986406	0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2986407	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2986408	0.88[JPT][hapmap]
rs2986413	0.88[JPT][hapmap]
rs2986421	0.88[JPT][hapmap]
rs3118498	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs496653	0.93[CHB][hapmap];0.94[ASN][1000 genomes]
rs511776	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs520658	0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs522436	0.91[ASN][1000 genomes]
rs568932	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724714	0.85[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs733567	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746124	0.93[GIH][hapmap]
rs7808	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984690	0.85[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv430371	chr11:34975067-35111292	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv1826391	chr11:35000983-35098193	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv897215	chr11:35009233-35048359	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv540999	chr11:35021936-35185471	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1326947	APIP	cis	lymphoblastoid	seeQTL
rs1326947	TRIM44	cis	parietal	SCAN
rs1326947	APIP	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34985200-35026600	Weak transcription	Colonic Mucosa	Colon
2	chr11:35000600-35035000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:35000800-35031000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:35007000-35026600	Weak transcription	Fetal Intestine Small	intestine
5	chr11:35007000-35028000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:35007000-35029800	Weak transcription	Esophagus	oesophagus
7	chr11:35007200-35035200	Weak transcription	Fetal Stomach	stomach
8	chr11:35007400-35026600	Weak transcription	Fetal Intestine Large	intestine
9	chr11:35007400-35026800	Weak transcription	Fetal Brain Female	brain
10	chr11:35007400-35027800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr11:35008600-35025200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr11:35008600-35026600	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:35008600-35026600	Weak transcription	Pancreas	Pancrea
14	chr11:35008600-35030800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:35009000-35025200	Weak transcription	Aorta	Aorta
16	chr11:35009000-35028000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:35009400-35026600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:35009400-35026800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:35011200-35025000	Weak transcription	NH-A	brain
20	chr11:35011400-35028200	Weak transcription	HSMMtube	muscle
21	chr11:35011600-35026800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:35016600-35025000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:35016800-35026600	Weak transcription	Liver	Liver
24	chr11:35016800-35026800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:35017200-35030800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:35019800-35035400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:35020000-35025000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:35020000-35028000	Weak transcription	Small Intestine	intestine
29	chr11:35020000-35030400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:35020200-35026600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:35020200-35028200	Weak transcription	Fetal Lung	lung
32	chr11:35020200-35028400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:35020200-35029800	Weak transcription	NHDF-Ad	bronchial
34	chr11:35020400-35025000	Weak transcription	Osteobl	bone
35	chr11:35020600-35025200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:35021400-35026600	Weak transcription	Stomach Mucosa	stomach
37	chr11:35021400-35026600	Weak transcription	NHEK	skin
38	chr11:35021400-35029400	Weak transcription	Hela-S3	cervix
39	chr11:35021800-35025000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:35021800-35026800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:35022000-35026800	Weak transcription	Left Ventricle	heart
42	chr11:35022000-35027400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr11:35022000-35028000	Weak transcription	Gastric	stomach
44	chr11:35024400-35025600	Enhancers	GM12878-XiMat	blood
45	chr11:35024400-35025800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:35024600-35025000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:35024600-35025000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:35024600-35025400	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr11:35024600-35025400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:35024600-35025400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links