Variant report

Variant	rs162116
Chromosome Location	chr19:52871902-52871903
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12976751	0.82[LWK][hapmap]
rs162118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs162119	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs184922	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs2241586	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[MKK][hapmap]
rs2244427	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2244428	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs321937	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs321938	0.82[JPT][hapmap]
rs707312	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707313	0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs780732	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription 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	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS 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	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs162116	LOC284379	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52861800-52872200	ZNF genes & repeats	Fetal Lung	lung
3	chr19:52865200-52875400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:52866600-52872200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:52866600-52875400	ZNF genes & repeats	Liver	Liver
6	chr19:52867200-52872400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:52867600-52872200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
8	chr19:52867800-52872200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:52869800-52872600	Weak transcription	Fetal Kidney	kidney
10	chr19:52869800-52872800	Weak transcription	Gastric	stomach
11	chr19:52870000-52872800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:52870000-52872800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:52870000-52872800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:52870000-52872800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:52870000-52872800	Weak transcription	Aorta	Aorta
16	chr19:52870000-52872800	Weak transcription	Fetal Brain Male	brain
17	chr19:52870000-52872800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr19:52870200-52872800	Weak transcription	Brain Angular Gyrus	brain
19	chr19:52870200-52872800	Weak transcription	Brain Anterior Caudate	brain
20	chr19:52870200-52872800	Weak transcription	Brain Substantia Nigra	brain
21	chr19:52870200-52872800	Weak transcription	Ovary	ovary
22	chr19:52870800-52872000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
23	chr19:52871000-52872600	Weak transcription	Brain Germinal Matrix	brain
24	chr19:52871000-52872600	Weak transcription	Fetal Brain Female	brain
25	chr19:52871000-52872800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:52871000-52872800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:52871000-52872800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:52871000-52872800	Weak transcription	Colon Smooth Muscle	Colon
29	chr19:52871200-52872800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:52871200-52872800	Weak transcription	Brain Hippocampus Middle	brain
31	chr19:52871200-52876400	Weak transcription	Dnd41	blood
32	chr19:52871800-52872600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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