Variant report

Variant	rs1952293
Chromosome Location	chr9:18822456-18822457
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10756990	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1980867	0.80[ASN][1000 genomes]
rs2163999	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6475255	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6475256	0.95[CEU][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7026429	0.95[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7037112	0.81[ASN][1000 genomes]
rs7041341	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs718452	0.86[AMR][1000 genomes]
rs7849165	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7873880	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs934469	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	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	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1952293	IFNA13	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18788000-18825200	Weak transcription	HUVEC	blood vessel
2	chr9:18800000-18824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:18806400-18826000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:18806600-18824200	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:18807000-18824000	Weak transcription	Gastric	stomach
6	chr9:18814600-18824400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:18815400-18829200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:18817000-18823200	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr9:18817000-18823800	Strong transcription	Osteobl	bone
10	chr9:18817000-18824200	Strong transcription	NHDF-Ad	bronchial
11	chr9:18817000-18824400	Strong transcription	HSMM	muscle
12	chr9:18818000-18825000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:18818000-18845200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:18818200-18828800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:18818400-18825000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:18818600-18824400	Weak transcription	Aorta	Aorta
17	chr9:18819000-18824400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:18819000-18825000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:18819000-18825000	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:18819200-18825000	Weak transcription	HSMMtube	muscle
21	chr9:18821600-18823200	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr9:18821600-18825400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr9:18821800-18822600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr9:18821800-18822600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr9:18821800-18822600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr9:18821800-18823800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:18822000-18822600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr9:18822000-18823000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr9:18822000-18823000	Enhancers	Hela-S3	cervix
30	chr9:18822000-18823400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:18822000-18826800	Enhancers	Fetal Heart	heart
32	chr9:18822200-18822600	Enhancers	Fetal Stomach	stomach
33	chr9:18822200-18822600	Enhancers	HepG2	liver
34	chr9:18822200-18822600	Enhancers	NHLF	lung
35	chr9:18822200-18822800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:18822200-18823000	Enhancers	Rectal Smooth Muscle	rectum
37	chr9:18822200-18823000	Weak transcription	Stomach Mucosa	stomach
38	chr9:18822200-18823200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr9:18822200-18824200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:18822200-18825200	Weak transcription	NH-A	brain
41	chr9:18822400-18822600	Enhancers	Fetal Thymus	thymus
42	chr9:18822400-18823600	Enhancers	Duodenum Mucosa	Duodenum
43	chr9:18822400-18823600	Enhancers	Sigmoid Colon	Sigmoid Colon

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