Variant report

Variant	rs10183541
Chromosome Location	chr2:50716768-50716769
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:50712217..50714362-chr2:50715383..50718092,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1006138	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1014430	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10168080	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10168838	0.90[JPT][hapmap]
rs10176959	0.94[ASN][1000 genomes]
rs10184537	1.00[YRI][hapmap]
rs10187846	0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10190305	0.88[ASN][1000 genomes]
rs10191072	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1019318	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10199840	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10207057	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10210592	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10211193	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1030050	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12713104	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13012186	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13034257	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1984957	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041868	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2041869	0.90[ASN][1000 genomes]
rs2058751	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2058752	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2066948	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2111065	0.90[ASN][1000 genomes]
rs2111066	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs2111069	0.93[ASN][1000 genomes]
rs2160448	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2160449	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2216171	0.90[ASN][1000 genomes]
rs6545172	0.90[ASN][1000 genomes]
rs6545173	0.91[ASN][1000 genomes]
rs6545174	0.98[ASN][1000 genomes]
rs6545175	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545176	0.95[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs6545177	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545178	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6707531	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs6713061	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6722389	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6732076	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6753552	0.98[ASN][1000 genomes]
rs7564428	0.99[ASN][1000 genomes]
rs7566514	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs759503	0.85[ASN][1000 genomes]
rs7595040	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs759505	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs759506	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv933786	chr2:50628354-50780185	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1010510	chr2:50649641-51011565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv535694	chr2:50649641-51011565	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv532650	chr2:50675808-51136752	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv491644	chr2:50680795-50892906	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv498102	chr2:50680795-50937503	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv2724	chr2:50688876-50734321	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv532651	chr2:50712339-50758351	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv532681	chr2:50715261-51172182	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10183541	SH3BGRL2	trans	parietal	SCAN
rs10183541	RHOQ	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50691600-50718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:50699000-50742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:50704400-50718600	Weak transcription	Fetal Brain Male	brain
4	chr2:50706200-50719000	Weak transcription	Stomach Mucosa	stomach
5	chr2:50706600-50719400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:50712600-50718800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:50713400-50718200	Weak transcription	Brain Angular Gyrus	brain
8	chr2:50714600-50718600	Weak transcription	Brain Anterior Caudate	brain
9	chr2:50716000-50717800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:50716200-50717000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:50716200-50718600	Weak transcription	Brain Germinal Matrix	brain
12	chr2:50716400-50717400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:50716400-50719200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:50716600-50719000	Weak transcription	Fetal Brain Female	brain

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