Variant report

Variant	rs1518040
Chromosome Location	chr1:223497150-223497151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223471938..223473458-chr1:223497150..223499757,2	K562	blood:
2	chr1:223497129..223500114-chr1:223509294..223511393,2	K562	blood:
3	chr1:223496498..223499043-chr1:223513776..223516102,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1341289	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1539047	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17163789	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17163816	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17163818	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17163831	0.84[LWK][hapmap]
rs17487717	0.91[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs1829308	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1829309	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1850562	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1856933	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1935037	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1949441	0.86[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs2096082	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2138970	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2176504	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2176505	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2176506	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2203763	0.83[LWK][hapmap]
rs34238669	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34468460	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4661238	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4661239	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61838234	0.81[AFR][1000 genomes]
rs61838235	0.81[AFR][1000 genomes]
rs61838236	0.81[AFR][1000 genomes]
rs61838237	0.81[AFR][1000 genomes]
rs61838241	0.81[AFR][1000 genomes]
rs66531524	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66768536	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66867621	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67707169	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7536652	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs7541162	0.81[AFR][1000 genomes]
rs825127	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs825128	0.81[AFR][1000 genomes]
rs825131	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1518040	SUSD4	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223495200-223498400	Enhancers	Fetal Thymus	thymus
2	chr1:223495600-223498400	Enhancers	Primary T cells from cord blood	blood
3	chr1:223495600-223498400	Enhancers	Thymus	Thymus
4	chr1:223495800-223498200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:223496000-223497200	Enhancers	Ovary	ovary
6	chr1:223496000-223498000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr1:223496000-223498200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr1:223496000-223498600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:223496200-223497400	Weak transcription	Fetal Heart	heart
10	chr1:223496200-223498200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr1:223496200-223498200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr1:223496400-223498200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:223496400-223498200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:223496400-223498400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:223496600-223497400	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:223496800-223497200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:223496800-223497200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:223496800-223497600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:223496800-223497600	Flanking Active TSS	Dnd41	blood
20	chr1:223497000-223497200	Enhancers	Esophagus	oesophagus
21	chr1:223497000-223497200	Enhancers	Pancreas	Pancrea
22	chr1:223497000-223497200	Enhancers	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links