Variant report

Variant	rs10840316
Chromosome Location	chr11:9912131-9912132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10743120	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10770070	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10770073	0.89[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10840320	0.96[ASN][1000 genomes]
rs10840321	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10840322	0.90[ASN][1000 genomes]
rs11042527	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11042531	0.96[ASN][1000 genomes]
rs11042532	0.97[ASN][1000 genomes]
rs11042541	0.90[ASN][1000 genomes]
rs12362504	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12365540	0.91[AFR][1000 genomes]
rs12796169	0.84[LWK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs12800780	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2017503	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs35396321	0.87[AFR][1000 genomes]
rs35749184	0.84[EUR][1000 genomes]
rs4334006	0.91[AFR][1000 genomes]
rs4445629	0.88[AFR][1000 genomes]
rs4498988	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs4910067	0.87[CEU][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs4910073	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910074	1.00[JPT][hapmap]
rs4910076	0.84[AFR][1000 genomes]
rs55813311	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56138865	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56165961	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56981829	0.88[EUR][1000 genomes]
rs60975667	0.84[EUR][1000 genomes]
rs6483805	0.89[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7122293	0.87[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs7126063	0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs71463738	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7930281	0.82[LWK][hapmap];0.85[AFR][1000 genomes]
rs7931062	0.89[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7936793	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7942326	0.87[EUR][1000 genomes]
rs7948688	0.85[AFR][1000 genomes]
rs7949582	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7950839	0.88[EUR][1000 genomes]
rs9300099	0.90[ASN][1000 genomes]
rs9300100	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332432	0.82[JPT][hapmap]
rs9919605	0.80[LWK][hapmap];0.81[AFR][1000 genomes]
rs9919609	0.85[AFR][1000 genomes]
rs9919617	0.87[AFR][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	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	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10840316	WDR61	trans	cerebellum	SCAN
rs10840316	SWAP70	cis	parietal	SCAN
rs10840316	LMO1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9878400-9916200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr11:9878800-9952200	Weak transcription	Aorta	Aorta
3	chr11:9880200-9913200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:9880600-9914800	Weak transcription	Placenta	Placenta
5	chr11:9882400-9929600	Weak transcription	Primary T cells from cord blood	blood
6	chr11:9890600-9915200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:9891400-9916800	Weak transcription	Primary B cells from cord blood	blood
8	chr11:9891800-9916600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:9892200-9914600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:9892400-9914400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:9892400-9914600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:9892400-9921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:9894200-9915200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr11:9894400-9916600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr11:9894400-9978600	Weak transcription	Left Ventricle	heart
16	chr11:9897000-9915000	Weak transcription	HSMMtube	muscle
17	chr11:9898200-9914800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:9898200-9917000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:9898400-9913800	Weak transcription	Fetal Stomach	stomach
20	chr11:9898600-9914800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:9898800-9915200	Weak transcription	Fetal Intestine Small	intestine
22	chr11:9899400-9915000	Weak transcription	Liver	Liver
23	chr11:9900600-9915000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:9901200-9915000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:9901200-9916600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:9902200-9917400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr11:9902400-9913000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:9903400-9915000	Weak transcription	Fetal Muscle Leg	muscle
29	chr11:9903600-9915200	Weak transcription	Ovary	ovary
30	chr11:9903600-9916600	Weak transcription	Fetal Lung	lung
31	chr11:9903800-9914600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr11:9904000-9937000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:9906000-9915000	Weak transcription	Fetal Intestine Large	intestine
34	chr11:9906400-9912800	Weak transcription	NHLF	lung
35	chr11:9906400-9914800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:9906400-9915000	Weak transcription	Osteobl	bone
37	chr11:9906800-9920400	Weak transcription	HUVEC	blood vessel
38	chr11:9907000-9914800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:9908400-9915000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:9909200-9915000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:9909400-9915000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr11:9909400-9916800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:9909600-9914800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:9909800-9916600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:9910000-9954600	Weak transcription	Pancreas	Pancrea
46	chr11:9910200-9921000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr11:9910800-9914600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr11:9910800-9915000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr11:9910800-9915000	Weak transcription	HSMM	muscle
50	chr11:9911000-9914800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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