Variant report

Variant	rs3843001
Chromosome Location	chr10:49798033-49798034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10491036	1.00[JPT][hapmap]
rs10491037	1.00[JPT][hapmap]
rs10491038	1.00[JPT][hapmap]
rs1075811	1.00[JPT][hapmap]
rs11593803	1.00[JPT][hapmap]
rs1373786	1.00[JPT][hapmap]
rs1373792	1.00[JPT][hapmap]
rs1445167	1.00[JPT][hapmap]
rs17010841	1.00[JPT][hapmap]
rs17010845	1.00[JPT][hapmap]
rs1814474	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1838577	1.00[JPT][hapmap]
rs1838578	1.00[JPT][hapmap]
rs2004405	0.87[ASN][1000 genomes]
rs2120909	1.00[JPT][hapmap]
rs2377518	1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2377519	1.00[JPT][hapmap]
rs2377520	0.89[AFR][1000 genomes]
rs2889659	0.88[ASW][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MKK][hapmap]
rs2894170	0.87[ASN][1000 genomes]
rs3843000	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3844200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851549	1.00[JPT][hapmap]
rs3851551	0.90[AFR][1000 genomes]
rs4282942	1.00[JPT][hapmap]
rs4320911	1.00[JPT][hapmap]
rs4838427	1.00[JPT][hapmap]
rs4838628	1.00[JPT][hapmap]
rs4838629	1.00[JPT][hapmap]
rs7075804	1.00[JPT][hapmap]
rs7085095	1.00[JPT][hapmap]
rs7896935	1.00[CHB][hapmap]
rs7906475	1.00[CHB][hapmap]
rs7909968	1.00[JPT][hapmap]
rs7911853	1.00[JPT][hapmap]
rs870353	1.00[JPT][hapmap]
rs935264	1.00[JPT][hapmap]
rs935285	1.00[JPT][hapmap]
rs935287	1.00[JPT][hapmap]
rs935288	1.00[JPT][hapmap]
rs935291	1.00[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3843001	SYT15	cis	parietal	SCAN
rs3843001	CAPN10	trans	cerebellum	SCAN

Chromatin state (count:39 , 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	chr10:49796600-49798400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr10:49796600-49799000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:49796800-49798400	Enhancers	Esophagus	oesophagus
18	chr10:49796800-49798400	Enhancers	NHEK	skin
19	chr10:49796800-49798600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr10:49796800-49799200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr10:49796800-49799400	Enhancers	HUVEC	blood vessel
22	chr10:49797000-49798200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:49797000-49798400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:49797000-49798600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr10:49797200-49798200	Weak transcription	Left Ventricle	heart
26	chr10:49797200-49798400	Enhancers	Brain Anterior Caudate	brain
27	chr10:49797400-49799400	Enhancers	HSMM	muscle
28	chr10:49797400-49812200	Weak transcription	Right Atrium	heart
29	chr10:49797600-49798600	Enhancers	HSMMtube	muscle
30	chr10:49797600-49798800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
31	chr10:49797800-49798600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:49797800-49799400	Enhancers	NH-A	brain
33	chr10:49797800-49802600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr10:49798000-49798200	Enhancers	Spleen	Spleen
35	chr10:49798000-49798400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr10:49798000-49798800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:49798000-49799200	Enhancers	Osteobl	bone
38	chr10:49798000-49799400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr10:49798000-49799600	Genic enhancers	Muscle Satellite Cultured Cells	--

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