Variant report

Variant	rs10820972
Chromosome Location	chr9:92930111-92930112
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10992311	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992324	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12341265	0.85[EUR][1000 genomes]
rs1331702	0.83[EUR][1000 genomes]
rs1331703	0.83[EUR][1000 genomes]
rs28571209	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28680232	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28820642	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56822056	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7025302	0.85[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7037744	0.85[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7468504	0.88[ASN][1000 genomes]
rs9785239	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv614852	chr9:92786722-93100550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv893563	chr9:92816727-92967125	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1051180	chr9:92869383-93141038	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv540169	chr9:92869383-93141038	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv482531	chr9:92907692-93096360	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10820972	SEMA4D	cis	cerebellum	SCAN
rs10820972	SEMA4D	cis	parietal	SCAN
rs10820972	NAA35	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92925200-92933200	Weak transcription	Esophagus	oesophagus
2	chr9:92927600-92930600	Enhancers	Pancreas	Pancrea
3	chr9:92927600-92931400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr9:92927800-92931200	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr9:92928000-92931400	Enhancers	Duodenum Mucosa	Duodenum
6	chr9:92929200-92930200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:92929200-92935200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:92930000-92930200	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr9:92930000-92930400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:92930000-92930400	Enhancers	Small Intestine	intestine
11	chr9:92930000-92930600	Enhancers	Fetal Lung	lung
12	chr9:92930000-92931200	Enhancers	Colonic Mucosa	Colon
13	chr9:92930000-92931800	Enhancers	Fetal Intestine Large	intestine
14	chr9:92930000-92932200	Enhancers	Stomach Mucosa	stomach

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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