Variant report

Variant	rs11169807
Chromosome Location	chr12:39244161-39244162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10444553	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs10876208	0.82[EUR][1000 genomes]
rs11169258	1.00[ASW][hapmap]
rs11169482	1.00[ASW][hapmap]
rs11169768	0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs1400280	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs1400285	0.86[EUR][1000 genomes]
rs1403521	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs1516558	0.92[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1523118	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs2388172	0.92[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs3759139	1.00[ASW][hapmap]
rs3803020	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs4384412	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs4595586	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4616077	1.00[ASW][hapmap]
rs4768388	0.97[EUR][1000 genomes]
rs56149694	0.95[EUR][1000 genomes]
rs7314227	0.83[EUR][1000 genomes]
rs7315271	1.00[ASW][hapmap]
rs7962363	0.92[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap]
rs7970097	0.92[CEU][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11169807	SYT10	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39203200-39276000	Weak transcription	Aorta	Aorta
2	chr12:39204000-39284800	Weak transcription	Lung	lung
3	chr12:39206600-39249200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:39221800-39251800	Weak transcription	Liver	Liver
5	chr12:39229400-39252200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:39232400-39247600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:39233200-39245800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:39238800-39271600	Weak transcription	NHEK	skin
9	chr12:39239200-39284000	Weak transcription	Hela-S3	cervix
10	chr12:39241400-39244200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:39242200-39244600	Weak transcription	NHDF-Ad	bronchial
12	chr12:39242200-39245400	Weak transcription	GM12878-XiMat	blood
13	chr12:39242200-39252400	Weak transcription	Ovary	ovary
14	chr12:39242400-39244200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:39242400-39248200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr12:39242400-39251200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:39243800-39244200	Enhancers	Left Ventricle	heart
18	chr12:39243800-39244400	Enhancers	Osteobl	bone
19	chr12:39243800-39244600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:39244000-39244200	Enhancers	Spleen	Spleen
21	chr12:39244000-39244600	Enhancers	Right Atrium	heart
22	chr12:39244000-39244800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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