Variant report

Variant	rs17161993
Chromosome Location	chr1:223469313-223469314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1095170	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1341291	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1356481	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1356482	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1518044	0.97[LWK][hapmap];1.00[YRI][hapmap]
rs17161994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163762	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17163773	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17163774	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17518279	0.89[ASW][hapmap];0.84[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2203763	0.84[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2678367	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2795063	1.00[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34013846	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34283624	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34782082	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34788475	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35133329	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35345711	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41371046	0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4661252	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6662301	0.94[AMR][1000 genomes];0.95[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
rs17161993	SUSD4	cis	parietal	SCAN

Chromatin state (count:10 , 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	chr1:223468600-223472000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:223469200-223472000	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links