Variant report

Variant	rs17536908
Chromosome Location	chr12:32661218-32661219
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10506090	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10506093	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10771961	0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10844222	0.81[MEX][hapmap]
rs10844223	0.81[MEX][hapmap]
rs10844224	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10844226	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10844227	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10844228	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10844229	0.85[ASN][1000 genomes]
rs10844230	0.89[ASN][1000 genomes]
rs10844231	0.89[ASN][1000 genomes]
rs10844232	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10844234	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11052040	0.91[ASN][1000 genomes]
rs11052041	0.89[ASN][1000 genomes]
rs11052042	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052046	0.89[ASN][1000 genomes]
rs11052052	0.85[ASN][1000 genomes]
rs11052053	0.89[ASN][1000 genomes]
rs11052055	0.94[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11052079	1.00[JPT][hapmap]
rs11608343	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12305379	1.00[YRI][hapmap]
rs12322132	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12366886	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1500875	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1500876	0.81[MEX][hapmap]
rs16920058	1.00[JPT][hapmap]
rs16920125	1.00[JPT][hapmap]
rs1909509	1.00[JPT][hapmap]
rs2036266	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2133943	0.81[MEX][hapmap]
rs2133944	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2728686	1.00[YRI][hapmap]
rs4105685	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4520681	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs61928965	0.93[ASN][1000 genomes]
rs73092002	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73094103	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7953022	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7964715	0.89[ASN][1000 genomes]
rs7967306	0.89[ASN][1000 genomes]
rs7967702	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7970857	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7974089	0.91[ASN][1000 genomes]
rs7975311	1.00[YRI][hapmap]
rs7977101	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7980571	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv898970	chr12:32622097-32680236	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17536908	SYT10	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32655200-32661600	Weak transcription	Spleen	Spleen
2	chr12:32655200-32686000	Weak transcription	Lung	lung
3	chr12:32656000-32666000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:32656000-32668000	Weak transcription	Fetal Thymus	thymus
5	chr12:32656200-32662600	Weak transcription	HepG2	liver
6	chr12:32656200-32668000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:32656400-32685800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:32657000-32661800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:32657200-32662200	Enhancers	Fetal Heart	heart
10	chr12:32657400-32661400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr12:32658600-32667800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:32658600-32682000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:32659200-32664400	Weak transcription	NHEK	skin
14	chr12:32659400-32665800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:32659400-32667000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:32659600-32661400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:32659600-32662600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:32659600-32662600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:32659600-32663400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr12:32659600-32668000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:32659600-32675200	Weak transcription	Fetal Stomach	stomach
22	chr12:32659800-32661600	Weak transcription	Fetal Brain Male	brain
23	chr12:32659800-32662800	Weak transcription	Fetal Intestine Large	intestine
24	chr12:32659800-32665400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:32659800-32669000	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:32660200-32661400	Enhancers	Brain Cingulate Gyrus	brain
27	chr12:32660200-32662200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr12:32660400-32661400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr12:32660400-32661600	Enhancers	HUVEC	blood vessel
30	chr12:32660400-32661800	Enhancers	Adipose Nuclei	Adipose
31	chr12:32660400-32662000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:32660400-32662200	Enhancers	Stomach Mucosa	stomach
33	chr12:32660600-32661800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:32660600-32661800	Enhancers	Fetal Muscle Leg	muscle
35	chr12:32660600-32662600	Weak transcription	Fetal Intestine Small	intestine
36	chr12:32660600-32664200	Enhancers	Liver	Liver
37	chr12:32660800-32661600	Enhancers	Brain Substantia Nigra	brain
38	chr12:32660800-32661800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:32660800-32661800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:32660800-32661800	Enhancers	Brain Angular Gyrus	brain
41	chr12:32660800-32661800	Enhancers	Gastric	stomach
42	chr12:32660800-32661800	Enhancers	Psoas Muscle	Psoas
43	chr12:32660800-32661800	Enhancers	Right Ventricle	heart
44	chr12:32660800-32662000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:32660800-32662000	Enhancers	Fetal Lung	lung
46	chr12:32660800-32662000	Enhancers	Ovary	ovary
47	chr12:32660800-32662000	Enhancers	Right Atrium	heart
48	chr12:32660800-32663000	Enhancers	Left Ventricle	heart
49	chr12:32661000-32661600	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr12:32661000-32661800	Enhancers	Pancreas	Pancrea

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