Variant report

Variant	rs1208578
Chromosome Location	chr10:38233864-38233865
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10508861	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1208619	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1208621	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12243792	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12265979	0.95[CEU][hapmap]
rs12412402	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12413083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[ASN][1000 genomes]
rs12414618	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1735625	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17608725	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176831	0.86[EUR][1000 genomes]
rs176832	0.84[EUR][1000 genomes]
rs176890	0.90[CEU][hapmap]
rs1779073	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs200909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs200913	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs200914	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200941	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200944	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2021651	0.84[EUR][1000 genomes]
rs2178958	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293962	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2472153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2472159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2472160	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2474542	0.89[ASN][1000 genomes]
rs2474545	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2474553	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2480521	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2489166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2504137	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2505218	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2738221	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2753883	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55742761	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59486180	0.81[EUR][1000 genomes]
rs766362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7895468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9418311	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1052703	chr10:38174640-38266472	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1208578	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs1208578	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38201400-38234200	Weak transcription	Left Ventricle	heart
2	chr10:38201400-38240000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr10:38220800-38241000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr10:38221400-38234200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:38223400-38241000	Weak transcription	Brain Angular Gyrus	brain
6	chr10:38223600-38240600	Weak transcription	Aorta	Aorta
7	chr10:38227400-38241000	Weak transcription	Colon Smooth Muscle	Colon
8	chr10:38227400-38241600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr10:38227600-38238000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr10:38227800-38239200	Weak transcription	Adipose Nuclei	Adipose
11	chr10:38229400-38238000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:38229400-38241000	Weak transcription	Fetal Brain Male	brain
13	chr10:38229600-38240600	Weak transcription	Right Ventricle	heart
14	chr10:38230000-38234400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr10:38230400-38236800	Weak transcription	Ovary	ovary
16	chr10:38231600-38238800	Weak transcription	Brain Anterior Caudate	brain
17	chr10:38231800-38234000	Weak transcription	Brain Germinal Matrix	brain
18	chr10:38231800-38238400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:38231800-38239600	Weak transcription	Brain Substantia Nigra	brain
20	chr10:38232000-38240200	Weak transcription	Fetal Brain Female	brain
21	chr10:38232400-38241000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:38232600-38236800	Weak transcription	Fetal Muscle Leg	muscle
23	chr10:38232600-38240400	Weak transcription	Fetal Lung	lung
24	chr10:38232800-38236800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr10:38232800-38238000	Weak transcription	Primary B cells from cord blood	blood
26	chr10:38233000-38237000	Weak transcription	Lung	lung
27	chr10:38233000-38239200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr10:38233000-38240000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr10:38233000-38241200	Weak transcription	Esophagus	oesophagus
30	chr10:38233200-38235000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:38233200-38238600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr10:38233200-38240400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr10:38233400-38240200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr10:38233400-38241000	Weak transcription	Spleen	Spleen
35	chr10:38233600-38234800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr10:38233800-38234800	Strong transcription	Brain Hippocampus Middle	brain

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