Variant report

Variant	rs3780223
Chromosome Location	chr9:18888920-18888921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10756994	0.82[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs10811053	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10811055	0.84[GIH][hapmap];0.90[JPT][hapmap]
rs10963814	0.93[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10963815	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10963816	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11794832	0.85[JPT][hapmap]
rs1368773	0.94[ASN][1000 genomes]
rs1579562	0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1594808	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2209778	0.82[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4977265	0.90[JPT][hapmap]
rs4977457	1.00[CEU][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4977458	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4977459	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs945440	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18878600-18895600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:18879800-18889800	Weak transcription	HSMMtube	muscle
3	chr9:18885200-18889600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:18885800-18896400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:18886200-18889600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:18886400-18889800	Weak transcription	NHLF	lung
7	chr9:18887000-18890000	Strong transcription	NH-A	brain
8	chr9:18887200-18891000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:18887800-18889200	Strong transcription	Fetal Stomach	stomach
10	chr9:18887800-18889800	Strong transcription	Aorta	Aorta
11	chr9:18887800-18889800	Strong transcription	HSMM	muscle
12	chr9:18888000-18889000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:18888000-18891000	Enhancers	Stomach Smooth Muscle	stomach
14	chr9:18888000-18892400	Weak transcription	Pancreas	Pancrea
15	chr9:18888200-18889800	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr9:18888200-18891200	Enhancers	Fetal Thymus	thymus
17	chr9:18888400-18889200	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:18888400-18891200	Enhancers	GM12878-XiMat	blood
19	chr9:18888600-18890200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:18888600-18894600	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:18888600-18896400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:18888800-18889600	Strong transcription	Osteobl	bone
23	chr9:18888800-18889800	Strong transcription	NHDF-Ad	bronchial
24	chr9:18888800-18890000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:18888800-18890200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:18888800-18890200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:18888800-18895400	Weak transcription	Rectal Mucosa Donor 31	rectum

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