Variant report

Variant	rs9843007
Chromosome Location	chr3:61207077-61207078
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10510864	0.83[CHD][hapmap]
rs11130821	0.86[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11130822	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11130826	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11130827	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11720254	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12492551	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1349798	0.83[ASN][1000 genomes]
rs1349799	0.83[ASN][1000 genomes]
rs1470035	0.94[ASW][hapmap];0.91[CEU][hapmap];0.88[LWK][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes]
rs1524017	0.87[ASN][1000 genomes]
rs1554599	0.90[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17064630	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17064653	0.87[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs17064657	0.83[CHD][hapmap]
rs17064660	0.87[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1916800	0.94[ASW][hapmap];0.91[CEU][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1916801	0.91[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1916802	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1980308	0.90[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1980309	0.90[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1980310	0.90[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1980311	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34515056	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35198002	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3915074	0.87[ASN][1000 genomes]
rs4296587	0.80[EUR][1000 genomes]
rs4535219	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs4605537	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4688354	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4688355	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4688359	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688379	0.83[EUR][1000 genomes]
rs6445197	0.81[EUR][1000 genomes]
rs6445198	0.81[EUR][1000 genomes]
rs6445199	0.81[EUR][1000 genomes]
rs6787292	0.85[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6787313	0.82[AFR][1000 genomes]
rs6809031	0.80[EUR][1000 genomes]
rs71296711	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7432943	0.85[AFR][1000 genomes]
rs7613368	0.82[ASN][1000 genomes]
rs896904	0.82[ASN][1000 genomes]
rs9832387	0.86[AFR][1000 genomes]
rs9832404	0.87[AFR][1000 genomes]
rs9844741	0.80[EUR][1000 genomes]
rs9846073	0.94[ASW][hapmap];0.91[CEU][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9850114	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9859004	0.80[EUR][1000 genomes]
rs9860681	0.81[AFR][1000 genomes]
rs9875827	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9882800	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv997718	chr3:61176349-61222975	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
10	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9843007	ADAMTS9	cis	parietal	SCAN
rs9843007	FHIT	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61201200-61221000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:61202400-61207600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:61203200-61207400	Weak transcription	Left Ventricle	heart
4	chr3:61203200-61209200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:61203200-61215400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:61203200-61222200	Weak transcription	Psoas Muscle	Psoas
7	chr3:61203400-61207600	Weak transcription	Gastric	stomach
8	chr3:61203400-61207600	Weak transcription	Ovary	ovary
9	chr3:61203400-61209200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:61203400-61213400	Weak transcription	Fetal Lung	lung
11	chr3:61203400-61225600	Weak transcription	Lung	lung
12	chr3:61203400-61225600	Weak transcription	Pancreas	Pancrea
13	chr3:61204200-61207400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:61204600-61207600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:61204800-61207600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:61206800-61208200	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr3:61207000-61207200	Enhancers	Duodenum Mucosa	Duodenum
18	chr3:61207000-61208200	Enhancers	Fetal Intestine Small	intestine
19	chr3:61207000-61211000	Enhancers	Fetal Brain Male	brain

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