Variant report

Variant	rs9547994
Chromosome Location	chr13:38219448-38219449
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1006416	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1028728	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11147662	0.86[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11618138	0.89[ASN][1000 genomes]
rs11619443	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11843893	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17197908	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17258466	0.92[ASN][1000 genomes]
rs1924298	0.92[ASN][1000 genomes]
rs2007577	0.81[ASN][1000 genomes]
rs2209230	0.92[ASN][1000 genomes]
rs28373781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28646275	0.82[EUR][1000 genomes]
rs3934220	0.92[ASN][1000 genomes]
rs4432141	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs56312513	0.82[EUR][1000 genomes]
rs56361602	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59082193	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61957472	0.84[ASN][1000 genomes]
rs61957483	0.92[ASN][1000 genomes]
rs73184517	0.92[ASN][1000 genomes]
rs7321585	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs7321872	0.95[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs7330679	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7333205	0.92[ASN][1000 genomes]
rs9532090	0.92[ASN][1000 genomes]
rs9532093	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9532095	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs9547953	0.84[ASN][1000 genomes]
rs9547958	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9547964	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9547965	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9547968	0.92[ASN][1000 genomes]
rs9547974	0.92[ASN][1000 genomes]
rs9547976	0.92[ASN][1000 genomes]
rs9547977	0.92[ASN][1000 genomes]
rs9547985	0.92[ASN][1000 genomes]
rs9547986	0.92[ASN][1000 genomes]
rs9547991	0.86[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9547992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9547996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9547997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9547998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9547999	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548003	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548008	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9548026	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv34109	chr13:37843819-38276391	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9547994	LOC646982	cis	parietal	SCAN
rs9547994	SMAD9	cis	cerebellum	SCAN
rs9547994	POSTN	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38207600-38224000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr13:38208000-38220600	Weak transcription	NH-A	brain
3	chr13:38210000-38219600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:38211400-38221200	Weak transcription	NHDF-Ad	bronchial
5	chr13:38211400-38275600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr13:38211600-38221200	Weak transcription	Ovary	ovary
7	chr13:38215600-38219600	Weak transcription	Fetal Brain Male	brain
8	chr13:38216000-38219600	Weak transcription	Fetal Brain Female	brain
9	chr13:38218200-38221200	Weak transcription	Osteobl	bone
10	chr13:38219000-38221600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr13:38219200-38219600	Enhancers	H9 Cell Line	embryonic stem cell
12	chr13:38219200-38219800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr13:38219200-38219800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:38219200-38219800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr13:38219200-38219800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:38219200-38219800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr13:38219200-38219800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr13:38219200-38219800	Enhancers	Fetal Kidney	kidney
19	chr13:38219200-38219800	Enhancers	Fetal Stomach	stomach
20	chr13:38219200-38220000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:38219200-38220000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr13:38219200-38220000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr13:38219200-38220000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:38219200-38220200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr13:38219200-38220400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr13:38219200-38220600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:38219200-38220800	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr13:38219200-38221200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr13:38219200-38221800	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr13:38219400-38219600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr13:38219400-38219600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:38219400-38219600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr13:38219400-38219600	Enhancers	Placenta	Placenta
34	chr13:38219400-38219800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr13:38219400-38219800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr13:38219400-38219800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr13:38219400-38219800	Enhancers	Fetal Heart	heart
38	chr13:38219400-38220000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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