Variant report

Variant	rs1361117
Chromosome Location	chr9:8615045-8615046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1033125	1.00[JPT][hapmap]
rs1033128	0.90[JPT][hapmap]
rs10815924	1.00[YRI][hapmap]
rs11788419	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs11788439	0.89[JPT][hapmap]
rs11792966	0.89[JPT][hapmap]
rs12682768	0.92[ASN][1000 genomes]
rs12683419	0.83[CHB][hapmap]
rs12683602	0.86[ASN][1000 genomes]
rs12685150	0.91[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs12686394	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12686827	0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12686852	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16924692	1.00[YRI][hapmap]
rs16928175	0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs16928179	0.91[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs16928185	0.92[ASN][1000 genomes]
rs16928187	0.91[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs16928206	0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16928219	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16928232	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16928234	0.90[CHD][hapmap];0.90[JPT][hapmap]
rs16928268	1.00[YRI][hapmap]
rs1999850	0.83[CHB][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs35286414	0.81[ASN][1000 genomes]
rs35565936	0.93[ASN][1000 genomes]
rs3750490	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs56024760	0.95[ASN][1000 genomes]
rs56025100	0.94[ASN][1000 genomes]
rs56411145	0.93[ASN][1000 genomes]
rs56774055	0.91[ASN][1000 genomes]
rs58151168	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60519226	0.81[ASN][1000 genomes]
rs62530700	0.92[ASN][1000 genomes]
rs62530702	0.93[ASN][1000 genomes]
rs62530704	0.93[ASN][1000 genomes]
rs62530705	0.93[ASN][1000 genomes]
rs62530706	0.91[ASN][1000 genomes]
rs62530708	0.93[ASN][1000 genomes]
rs62530709	0.93[ASN][1000 genomes]
rs62530710	0.93[ASN][1000 genomes]
rs7020239	0.83[CHB][hapmap]
rs7035431	0.83[CHB][hapmap]
rs7046119	0.94[CHD][hapmap];0.90[JPT][hapmap]
rs72698211	0.93[ASN][1000 genomes]
rs72698216	0.95[ASN][1000 genomes]
rs9792461	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1361117	RLN2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8586000-8618000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:8610600-8616800	Weak transcription	Ovary	ovary
3	chr9:8611400-8615600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr9:8612200-8615400	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr9:8612400-8615600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr9:8612400-8615600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr9:8612400-8615600	Enhancers	Brain Substantia Nigra	brain
8	chr9:8612600-8615600	Enhancers	Brain Hippocampus Middle	brain
9	chr9:8613400-8615200	Enhancers	Aorta	Aorta
10	chr9:8613400-8615600	Enhancers	Brain Cingulate Gyrus	brain
11	chr9:8613400-8615600	Enhancers	Fetal Heart	heart
12	chr9:8613600-8615400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:8613600-8615400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:8613600-8615400	Enhancers	Fetal Brain Male	brain
15	chr9:8613800-8615200	Enhancers	Brain Germinal Matrix	brain
16	chr9:8614400-8616000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:8614400-8627000	Weak transcription	Fetal Lung	lung
18	chr9:8614600-8615400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:8614600-8615600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:8614600-8615600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:8614600-8615600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr9:8614800-8615400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr9:8615000-8615200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr9:8615000-8615200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr9:8615000-8615200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr9:8615000-8615200	Enhancers	Brain Anterior Caudate	brain
27	chr9:8615000-8615200	Enhancers	Psoas Muscle	Psoas
28	chr9:8615000-8615400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:8615000-8615400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr9:8615000-8615400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:8615000-8615400	Enhancers	Brain Angular Gyrus	brain

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