Variant report

Variant	rs10963808
Chromosome Location	chr9:18857237-18857238
allele	A/G
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:17)

rs_ID	r²[population]
rs1001379	0.89[YRI][hapmap]
rs10117736	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10121884	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811050	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10963802	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963803	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963806	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16937142	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4977426	1.00[CEU][hapmap]
rs57229120	0.87[ASN][1000 genomes]
rs7033096	0.81[YRI][hapmap]
rs7039790	0.83[ASW][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.80[ASN][1000 genomes]
rs73423138	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7862903	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7874886	0.86[ASN][1000 genomes]
rs934483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[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	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892698	chr9:18830444-18905289	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10963808	MTNR1A	trans	brain	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18825600-18857400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:18827200-18861600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:18830800-18857400	Weak transcription	NHLF	lung
4	chr9:18845800-18861200	Weak transcription	Aorta	Aorta
5	chr9:18845800-18861800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:18847400-18858400	Weak transcription	NH-A	brain
7	chr9:18847800-18858600	Weak transcription	Gastric	stomach
8	chr9:18849400-18861200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:18849600-18857400	Weak transcription	Stomach Mucosa	stomach
10	chr9:18849600-18858200	Weak transcription	Right Atrium	heart
11	chr9:18850600-18858200	Weak transcription	Lung	lung
12	chr9:18850800-18860800	Weak transcription	Fetal Stomach	stomach
13	chr9:18851800-18861200	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:18852000-18857600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr9:18852000-18861200	Weak transcription	Left Ventricle	heart
16	chr9:18852400-18861200	Weak transcription	Right Ventricle	heart
17	chr9:18853400-18857400	Weak transcription	NHDF-Ad	bronchial
18	chr9:18853600-18861200	Weak transcription	HSMMtube	muscle
19	chr9:18853800-18858200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:18854000-18857600	Strong transcription	HSMM	muscle
21	chr9:18856200-18861200	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:18856200-18861200	Weak transcription	Ovary	ovary
23	chr9:18856400-18857400	Weak transcription	Fetal Heart	heart
24	chr9:18856600-18858200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:18856800-18858400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:18857000-18858000	Enhancers	Fetal Lung	lung
27	chr9:18857200-18857800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:18857200-18858600	Genic enhancers	Osteobl	bone
29	chr9:18857200-18858800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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