Variant report

Variant	rs7862903
Chromosome Location	chr9:18862658-18862659
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10121884	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811050	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10963802	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10963803	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10963806	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10963807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10963808	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]
rs4977426	1.00[CEU][hapmap]
rs57229120	0.90[ASN][1000 genomes]
rs7039790	0.94[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7874886	0.90[ASN][1000 genomes]
rs934483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[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
rs7862903	MTNR1A	trans	brain	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18858800-18876600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:18860600-18863200	Enhancers	Fetal Heart	heart
3	chr9:18860800-18864800	Enhancers	Fetal Lung	lung
4	chr9:18860800-18864800	Enhancers	Fetal Stomach	stomach
5	chr9:18861200-18862800	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr9:18861200-18862800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr9:18861200-18865000	Enhancers	Fetal Muscle Leg	muscle
8	chr9:18861600-18862800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:18861600-18863000	Enhancers	Fetal Muscle Trunk	muscle
10	chr9:18861600-18863800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:18861800-18862800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr9:18861800-18862800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr9:18861800-18863200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:18861800-18863200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:18862200-18862800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:18862200-18864400	Weak transcription	Brain Hippocampus Middle	brain
17	chr9:18862400-18862800	Enhancers	Adipose Nuclei	Adipose
18	chr9:18862400-18863000	Weak transcription	Aorta	Aorta
19	chr9:18862400-18863000	Weak transcription	Ovary	ovary
20	chr9:18862400-18863000	Weak transcription	HSMM	muscle
21	chr9:18862400-18863200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:18862400-18864000	Enhancers	Colon Smooth Muscle	Colon
23	chr9:18862400-18865600	Weak transcription	Fetal Brain Male	brain
24	chr9:18862400-18866800	Weak transcription	Right Ventricle	heart
25	chr9:18862600-18862800	Enhancers	NHLF	lung
26	chr9:18862600-18863000	Weak transcription	NH-A	brain
27	chr9:18862600-18863600	Genic enhancers	NHDF-Ad	bronchial
28	chr9:18862600-18864000	Weak transcription	Brain Anterior Caudate	brain
29	chr9:18862600-18864000	Enhancers	Stomach Smooth Muscle	stomach
30	chr9:18862600-18864400	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr9:18862600-18864800	Genic enhancers	Osteobl	bone
32	chr9:18862600-18865000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:18862600-18866200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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