Variant report

Variant	rs9646720
Chromosome Location	chr2:234847573-234847574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1003540	0.84[TSI][hapmap]
rs10166942	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs10189040	0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs10490012	0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10929319	0.87[MEX][hapmap]
rs11563216	0.87[MEX][hapmap]
rs13418652	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2108809	0.87[MEX][hapmap]
rs2302153	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362290	0.81[TSI][hapmap]
rs2362292	0.85[EUR][1000 genomes]
rs4663988	0.87[MEX][hapmap]
rs6431648	0.83[MEX][hapmap];0.89[TSI][hapmap]
rs6711120	0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs6740118	0.86[MEX][hapmap]
rs758275	0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs758276	0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs9646719	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876024	chr2:234842650-234856421	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9646720	NMUR1	cis	parietal	SCAN
rs9646720	COL6A3	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234841800-234847600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:234845400-234847800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:234845400-234851400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:234846600-234847600	Weak transcription	Gastric	stomach
5	chr2:234847400-234847600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:234847400-234847600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:234847400-234847800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr2:234847400-234847800	Bivalent Enhancer	Fetal Brain Male	brain
9	chr2:234847400-234848000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr2:234847400-234848000	Active TSS	Brain Germinal Matrix	brain
11	chr2:234847400-234848000	Active TSS	Fetal Brain Female	brain
12	chr2:234847400-234848200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:234847400-234848200	Bivalent/Poised TSS	Fetal Intestine Large	intestine

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Input of quick search could be:

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

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