Variant report

Variant	rs16928179
Chromosome Location	chr9:8602903-8602904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1033125	0.89[JPT][hapmap]
rs10815921	0.87[CEU][hapmap];0.94[EUR][1000 genomes]
rs10977230	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs11788419	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11788439	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11792966	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12682768	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12683419	0.92[CHB][hapmap]
rs12683602	0.85[ASN][1000 genomes]
rs12685150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12686394	0.85[ASN][1000 genomes]
rs12686827	0.90[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12686852	0.89[JPT][hapmap]
rs1337809	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs1361117	0.91[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs16928175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16928185	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16928187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16928206	0.82[CHB][hapmap];0.82[CHD][hapmap];0.94[ASN][1000 genomes]
rs16928219	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs16928232	0.88[JPT][hapmap]
rs16928234	0.84[CHD][hapmap]
rs1999850	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs35565936	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3750490	0.84[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs56024760	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56025100	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56411145	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56774055	0.94[ASN][1000 genomes]
rs58151168	0.94[ASN][1000 genomes]
rs60519226	0.80[ASN][1000 genomes]
rs62530700	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62530702	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62530704	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62530705	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62530706	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62530708	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62530709	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62530710	0.94[ASN][1000 genomes]
rs7020239	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs7035431	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs7043072	0.87[CEU][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs7046119	0.81[CHD][hapmap]
rs72698211	0.96[ASN][1000 genomes]
rs72698216	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9792461	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9792470	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv831504	chr9:8496277-8665773	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv892230	chr9:8569186-8643259	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv892231	chr9:8569186-8659757	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv613291	chr9:8573166-8615045	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv969747	chr9:8602441-8606501	Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16928179	RLN2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8576600-8613200	Weak transcription	Fetal Brain Female	brain
2	chr9:8583600-8605600	Weak transcription	Fetal Lung	lung
3	chr9:8583600-8613600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:8586000-8618000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:8588200-8613600	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:8597200-8615000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:8599800-8603000	Enhancers	Brain Cingulate Gyrus	brain
8	chr9:8600000-8603000	Enhancers	Brain Hippocampus Middle	brain
9	chr9:8600000-8603000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr9:8600000-8603000	Enhancers	Brain Substantia Nigra	brain
11	chr9:8600200-8615000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:8600800-8609800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:8601800-8604000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:8601800-8604000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:8601800-8613400	Weak transcription	Aorta	Aorta
16	chr9:8602200-8610000	Weak transcription	Brain Angular Gyrus	brain
17	chr9:8602400-8604400	Weak transcription	Brain Anterior Caudate	brain
18	chr9:8602400-8608600	Weak transcription	Fetal Heart	heart
19	chr9:8602800-8603000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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