Variant report

Variant	rs11042500
Chromosome Location	chr11:9830595-9830596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10743119	0.82[AFR][1000 genomes]
rs10770068	0.84[AFR][1000 genomes]
rs10840287	1.00[CHB][hapmap]
rs10840312	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10840315	1.00[CHB][hapmap]
rs10840325	1.00[CHB][hapmap]
rs10840327	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10840337	1.00[CHB][hapmap]
rs10840338	1.00[CHB][hapmap]
rs11042466	1.00[CHB][hapmap]
rs11042486	1.00[CHB][hapmap]
rs11042508	0.87[YRI][hapmap]
rs11042511	1.00[CHB][hapmap];0.87[YRI][hapmap]
rs11042526	1.00[CHB][hapmap]
rs11042543	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11042550	1.00[CHB][hapmap]
rs11042556	1.00[CHB][hapmap]
rs11042559	1.00[CHB][hapmap]
rs11042561	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11042571	1.00[CHB][hapmap]
rs11042579	1.00[CHB][hapmap]
rs11600183	1.00[CHB][hapmap]
rs11601212	1.00[CHD][hapmap]
rs11602515	1.00[CHB][hapmap]
rs11603291	1.00[CHD][hapmap]
rs11607582	1.00[CHB][hapmap]
rs12278797	0.89[AFR][1000 genomes]
rs12419564	1.00[CHB][hapmap]
rs12419923	1.00[CHB][hapmap]
rs12421200	1.00[CHB][hapmap]
rs12421878	1.00[CHB][hapmap]
rs12786236	1.00[CHB][hapmap]
rs12807017	1.00[CHB][hapmap]
rs12808226	1.00[CHB][hapmap]
rs17268414	0.81[ASW][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes]
rs17268632	1.00[CHB][hapmap]
rs17270804	1.00[CHB][hapmap]
rs17271847	1.00[CHB][hapmap]
rs17355675	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17355924	1.00[CHB][hapmap]
rs17356792	1.00[CHB][hapmap]
rs2403221	0.82[ASW][hapmap];0.85[AFR][1000 genomes]
rs360118	0.86[AFR][1000 genomes]
rs4909915	1.00[CHB][hapmap]
rs4910075	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4910080	1.00[CHB][hapmap]
rs4910081	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4910084	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4910487	1.00[CHB][hapmap]
rs4910497	1.00[CHB][hapmap]
rs4910505	1.00[CHB][hapmap]
rs7115754	1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap]
rs7131445	1.00[CHB][hapmap]
rs7937716	0.89[AFR][1000 genomes]
rs7943610	1.00[CHB][hapmap]
rs9645623	0.86[AMR][1000 genomes];1.00[ASN][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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11042500	PTH	cis	parietal	SCAN
rs11042500	NLRP10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9809600-9832600	Weak transcription	Colonic Mucosa	Colon
2	chr11:9812200-9862200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:9818600-9881400	Weak transcription	Spleen	Spleen
4	chr11:9824200-9837200	Weak transcription	Hela-S3	cervix
5	chr11:9824200-9867600	Weak transcription	Psoas Muscle	Psoas
6	chr11:9824400-9831800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:9824400-9841400	Weak transcription	Fetal Heart	heart
8	chr11:9824800-9831400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:9824800-9834400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:9825400-9838600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr11:9825800-9837400	Weak transcription	NH-A	brain
12	chr11:9825800-9837800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr11:9825800-9841600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:9826400-9830800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr11:9826600-9830800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:9826800-9830600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:9826800-9830800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:9826800-9868200	Weak transcription	Aorta	Aorta
19	chr11:9827000-9830800	Strong transcription	Fetal Muscle Leg	muscle
20	chr11:9827200-9830600	Strong transcription	Ovary	ovary
21	chr11:9827400-9830600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:9827800-9830800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:9827800-9830800	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr11:9828000-9830600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr11:9828000-9830600	Strong transcription	Adipose Nuclei	Adipose
26	chr11:9828400-9830600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr11:9828400-9830600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:9828400-9830800	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:9828400-9831600	Strong transcription	Fetal Intestine Large	intestine
30	chr11:9828600-9830600	Strong transcription	Fetal Brain Female	brain
31	chr11:9828600-9830600	Strong transcription	Fetal Lung	lung
32	chr11:9828600-9830600	Strong transcription	Left Ventricle	heart
33	chr11:9828600-9830600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:9828600-9830600	Strong transcription	NHLF	lung
35	chr11:9828600-9830800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:9828600-9830800	Strong transcription	Fetal Intestine Small	intestine
37	chr11:9828600-9830800	Strong transcription	Pancreas	Pancrea
38	chr11:9828600-9831000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:9828600-9834800	Strong transcription	HSMM	muscle
40	chr11:9828800-9830600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:9829000-9834400	Strong transcription	HSMMtube	muscle
42	chr11:9829200-9830800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:9829200-9830800	Strong transcription	Fetal Brain Male	brain
44	chr11:9829200-9832400	Weak transcription	Brain Anterior Caudate	brain
45	chr11:9829400-9832000	Strong transcription	Fetal Stomach	stomach
46	chr11:9829600-9830600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:9829600-9830600	Enhancers	Liver	Liver
48	chr11:9829600-9830800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:9829600-9830800	Enhancers	Colon Smooth Muscle	Colon
50	chr11:9829600-9832600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links