Variant report

Variant	rs9296300
Chromosome Location	chr6:39458150-39458151
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10214466	0.87[LWK][hapmap]
rs11961693	0.82[ASN][1000 genomes]
rs11962587	0.89[CHB][hapmap]
rs11964924	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs11968704	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs11969059	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs1546910	0.90[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs16892158	0.89[CHB][hapmap]
rs17457401	0.87[ASN][1000 genomes]
rs1927774	0.82[CHD][hapmap]
rs1952362	0.82[CHD][hapmap]
rs2026670	0.84[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2073134	0.90[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2235817	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs2273063	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs4236064	0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs4446568	0.84[ASN][1000 genomes]
rs4482968	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs4482969	0.81[ASN][1000 genomes]
rs4540261	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[MEX][hapmap]
rs4711598	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs4714253	0.84[CHB][hapmap]
rs4714255	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs4714256	0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs55860200	0.85[ASN][1000 genomes]
rs58087685	0.87[ASN][1000 genomes]
rs59724542	0.85[ASN][1000 genomes]
rs6901155	0.84[CHB][hapmap]
rs6919556	0.81[CHB][hapmap]
rs6930913	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9296298	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs9296299	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs9349120	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs9357306	0.89[ASN][1000 genomes]
rs9357307	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs9357308	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs9357309	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs9367008	0.95[CHB][hapmap]
rs9367009	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs9367012	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs9367014	0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs9367015	0.96[ASN][1000 genomes]
rs9367016	0.81[ASN][1000 genomes]
rs9367017	0.91[ASN][1000 genomes]
rs9369119	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs9369122	0.81[CHB][hapmap]
rs9380864	0.84[CHB][hapmap]
rs9380865	0.84[CHB][hapmap]
rs9380867	0.92[CHB][hapmap]
rs9380868	0.94[CHB][hapmap]
rs9380871	0.82[ASN][1000 genomes]
rs9380872	0.82[ASN][1000 genomes]
rs9380873	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs9380874	0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs9380875	0.81[ASN][1000 genomes]
rs9394592	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs9394594	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs9394595	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs9394598	0.89[CHB][hapmap]
rs9394599	0.95[CHB][hapmap];0.94[CHD][hapmap]
rs9394600	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs9394602	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs9394603	0.80[ASN][1000 genomes]
rs9394606	0.89[CHB][hapmap]
rs9462553	0.83[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs9471113	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9471118	0.94[ASN][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	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv428145	chr6:39404129-39460795	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv885823	chr6:39421715-39526867	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	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
rs9296300	SRPK1	cis	cerebellum	SCAN
rs9296300	RRP36	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39455200-39462800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:39455400-39459000	Enhancers	Fetal Lung	lung
3	chr6:39455400-39465200	Weak transcription	Right Atrium	heart
4	chr6:39456400-39459000	Weak transcription	Brain Angular Gyrus	brain
5	chr6:39456400-39461000	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:39456400-39461200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:39456800-39458200	Enhancers	Adipose Nuclei	Adipose
8	chr6:39456800-39468400	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:39457400-39458400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:39457800-39458200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:39457800-39458200	Enhancers	Fetal Kidney	kidney
12	chr6:39457800-39458600	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr6:39458000-39458200	Enhancers	Brain Cingulate Gyrus	brain
14	chr6:39458000-39458400	Enhancers	Stomach Smooth Muscle	stomach

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