Variant report

Variant	rs3851551
Chromosome Location	chr10:49797862-49797863
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10491036	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10491037	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10491038	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10491039	1.00[ASN][1000 genomes]
rs1075811	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs11593803	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345107	0.86[MEX][hapmap]
rs1373786	1.00[JPT][hapmap]
rs1373792	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1445167	1.00[JPT][hapmap]
rs17010841	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17010845	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1814474	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1838577	1.00[JPT][hapmap]
rs1838578	1.00[JPT][hapmap]
rs2120909	1.00[JPT][hapmap]
rs2377517	0.86[MEX][hapmap]
rs2377518	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377519	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377520	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2889659	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843000	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843001	0.94[ASW][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs3844200	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs3851549	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41281993	0.83[ASN][1000 genomes]
rs41281995	1.00[ASN][1000 genomes]
rs4282942	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4320911	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4375396	0.83[ASN][1000 genomes]
rs4572084	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838427	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4838628	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4838629	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs59135459	1.00[ASN][1000 genomes]
rs61092407	1.00[ASN][1000 genomes]
rs61235893	1.00[ASN][1000 genomes]
rs7075804	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs7085095	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs73300277	1.00[ASN][1000 genomes]
rs73300278	1.00[ASN][1000 genomes]
rs73300297	1.00[ASN][1000 genomes]
rs74130570	1.00[ASN][1000 genomes]
rs7909968	0.83[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7911853	1.00[JPT][hapmap]
rs870353	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs935264	1.00[JPT][hapmap]
rs935285	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs935287	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs935288	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs935291	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1046588	chr10:49790254-49806169	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3851551	CAPN10	trans	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49791400-49798400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr10:49794400-49810600	Enhancers	Brain Substantia Nigra	brain
3	chr10:49794800-49799200	Enhancers	Brain Hippocampus Middle	brain
4	chr10:49795000-49799400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr10:49795200-49803800	Enhancers	NHDF-Ad	bronchial
6	chr10:49795600-49798800	Genic enhancers	NHLF	lung
7	chr10:49795800-49798800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:49795800-49798800	Enhancers	Brain Cingulate Gyrus	brain
9	chr10:49795800-49798800	Enhancers	HMEC	breast
10	chr10:49796000-49798200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:49796000-49798400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:49796200-49799200	Enhancers	Fetal Stomach	stomach
13	chr10:49796200-49800600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:49796400-49799000	Enhancers	Brain Angular Gyrus	brain
15	chr10:49796600-49798000	Enhancers	Placenta	Placenta
16	chr10:49796600-49798400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr10:49796600-49799000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:49796800-49798400	Enhancers	Esophagus	oesophagus
19	chr10:49796800-49798400	Enhancers	NHEK	skin
20	chr10:49796800-49798600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr10:49796800-49799200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr10:49796800-49799400	Enhancers	HUVEC	blood vessel
23	chr10:49797000-49798000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr10:49797000-49798000	Flanking Active TSS	Osteobl	bone
25	chr10:49797000-49798200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:49797000-49798400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr10:49797000-49798600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr10:49797200-49798000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:49797200-49798000	Weak transcription	Spleen	Spleen
30	chr10:49797200-49798200	Weak transcription	Left Ventricle	heart
31	chr10:49797200-49798400	Enhancers	Brain Anterior Caudate	brain
32	chr10:49797400-49798000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:49797400-49798000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:49797400-49799400	Enhancers	HSMM	muscle
35	chr10:49797400-49812200	Weak transcription	Right Atrium	heart
36	chr10:49797600-49798600	Enhancers	HSMMtube	muscle
37	chr10:49797600-49798800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
38	chr10:49797800-49798600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:49797800-49799400	Enhancers	NH-A	brain
40	chr10:49797800-49802600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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