Variant report

Variant	rs41371046
Chromosome Location	chr1:223475159-223475160
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1356482	0.81[AFR][1000 genomes]
rs1518039	0.87[EUR][1000 genomes]
rs1518044	0.92[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1713221	0.88[EUR][1000 genomes]
rs17161993	0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs17161994	0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs17487717	0.84[JPT][hapmap]
rs17517806	0.82[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs1772277	0.81[EUR][1000 genomes]
rs1949441	0.84[JPT][hapmap]
rs2138967	0.87[EUR][1000 genomes]
rs2138968	0.86[EUR][1000 genomes]
rs2203763	0.91[MKK][hapmap]
rs34013846	0.81[AFR][1000 genomes]
rs35360808	0.87[EUR][1000 genomes]
rs35636122	0.87[EUR][1000 genomes]
rs712856	0.82[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9442041	0.82[CEU][hapmap];0.84[TSI][hapmap];0.86[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	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	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
rs41371046	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223466400-223480400	Weak transcription	Pancreas	Pancrea
2	chr1:223470000-223493200	Weak transcription	Esophagus	oesophagus
3	chr1:223472600-223476600	Weak transcription	Placenta	Placenta
4	chr1:223473000-223476000	Enhancers	Fetal Thymus	thymus
5	chr1:223473000-223476200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:223473000-223484400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:223473200-223476200	Enhancers	Thymus	Thymus
8	chr1:223473400-223476200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr1:223473400-223476200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:223474000-223476000	Enhancers	Primary T cells from cord blood	blood
11	chr1:223474000-223476000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr1:223474000-223476000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:223474000-223476000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:223474200-223476200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:223474200-223476200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:223474400-223475800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr1:223474800-223475400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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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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