Variant report

Variant	rs10820899
Chromosome Location	chr9:94482041-94482042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94474813..94478609-chr9:94479157..94482495,5	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10992057	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992058	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992059	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992060	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992061	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13292198	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073735	0.82[JPT][hapmap]
rs4073736	0.82[JPT][hapmap]
rs41308940	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67857232	0.91[ASN][1000 genomes]
rs7467403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869182	0.82[JPT][hapmap]
rs9409456	0.83[JPT][hapmap]
rs9409649	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10820899	ECM2	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94458000-94489800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:94473800-94483400	Weak transcription	K562	blood
3	chr9:94474200-94486000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:94476400-94485400	Weak transcription	Fetal Lung	lung
5	chr9:94477000-94483400	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:94477000-94487000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:94477200-94483000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:94477200-94483400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:94477200-94484600	Weak transcription	Ovary	ovary
10	chr9:94477200-94489800	Weak transcription	Right Atrium	heart
11	chr9:94477200-94496800	Weak transcription	NHLF	lung
12	chr9:94477200-94533000	Weak transcription	Fetal Kidney	kidney
13	chr9:94477800-94483200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:94477800-94483800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:94478800-94484400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:94478800-94484600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:94479400-94484400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:94480600-94484400	Weak transcription	Gastric	stomach
19	chr9:94480800-94482200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:94480800-94482200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:94480800-94483400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:94481200-94484400	Weak transcription	Fetal Intestine Small	intestine
23	chr9:94481800-94483800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:94481800-94484000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr9:94482000-94482400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:94482000-94483000	Weak transcription	Fetal Stomach	stomach
27	chr9:94482000-94484400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:94482000-94484400	Weak transcription	Fetal Intestine Large	intestine

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