Variant report

Variant	rs712856
Chromosome Location	chr1:223468336-223468337
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1400962	0.96[ASN][1000 genomes]
rs1418151	0.83[JPT][hapmap]
rs1518039	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1713221	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17517806	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1772270	0.96[ASN][1000 genomes]
rs1772271	0.96[ASN][1000 genomes]
rs1772277	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2138967	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2138968	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35360808	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35636122	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35737777	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs41371046	0.82[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9442041	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv516810	chr1:223468336-223468732	Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv518979	chr1:223468336-223488310	Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs712856	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223443800-223472600	Weak transcription	Gastric	stomach
2	chr1:223459000-223474200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr1:223460800-223473400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:223461200-223469600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:223464400-223472800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:223465800-223469600	Weak transcription	Esophagus	oesophagus
7	chr1:223466400-223471800	Weak transcription	Ovary	ovary
8	chr1:223466400-223480400	Weak transcription	Pancreas	Pancrea
9	chr1:223467200-223469200	Weak transcription	Primary T cells from cord blood	blood

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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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