Variant report

Variant	rs535599
Chromosome Location	chr9:92773125-92773126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13296044	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1373102	0.91[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1443358	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1443360	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35150414	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs501675	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs557789	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs601472	0.96[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs613212	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs627985	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs628020	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs633926	0.96[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs636460	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs650415	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs650882	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs661232	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs666603	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs679273	0.96[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs683669	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7018766	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7036231	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs704476	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs920752	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs535599	SEMA4D	cis	parietal	SCAN
rs535599	CKS2	cis	cerebellum	SCAN
rs535599	SEMA4D	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92765800-92775200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr9:92768000-92774800	Weak transcription	Fetal Intestine Small	intestine
3	chr9:92769000-92773400	Enhancers	Primary B cells from peripheral blood	blood
4	chr9:92770000-92773200	Enhancers	Primary hematopoietic stem cells	blood
5	chr9:92770800-92774800	Weak transcription	Fetal Intestine Large	intestine
6	chr9:92770800-92775000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:92770800-92775400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:92771800-92775400	Weak transcription	HSMMtube	muscle
9	chr9:92771800-92776400	Weak transcription	HSMM	muscle
10	chr9:92771800-92781400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:92772000-92773800	Enhancers	Primary B cells from cord blood	blood
12	chr9:92772000-92775200	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:92772000-92775200	Weak transcription	Stomach Mucosa	stomach
14	chr9:92772200-92780800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:92772400-92775200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr9:92772600-92775200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr9:92773000-92775200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:92773000-92775200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links