Variant report

Variant	rs17650849
Chromosome Location	chr12:45013986-45013987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10506251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182567	1.00[EUR][1000 genomes]
rs11182568	1.00[CEU][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes]
rs11182573	1.00[EUR][1000 genomes]
rs11182575	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11182578	1.00[EUR][1000 genomes]
rs11182582	1.00[EUR][1000 genomes]
rs11182593	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11182653	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs11612950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613236	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615599	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1452885	0.82[MEX][hapmap]
rs1452886	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17094881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17094886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17094892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17571971	1.00[CEU][hapmap];1.00[CHB][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]
rs17572590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17572765	1.00[CHB][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17574492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17574839	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17575480	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs17649873	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17651646	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17652715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17653092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17653542	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17654244	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs17654558	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17654689	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2408044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4768061	1.00[ASN][1000 genomes]
rs4768068	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768069	1.00[EUR][1000 genomes]
rs4768070	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768561	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768570	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs4768574	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs59098139	1.00[EUR][1000 genomes]
rs61671085	1.00[EUR][1000 genomes]
rs6582510	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6582511	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6582512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135950	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296595	1.00[ASN][1000 genomes]
rs7301676	1.00[ASN][1000 genomes]
rs7305652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73282400	1.00[ASN][1000 genomes]
rs73284070	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73284080	1.00[EUR][1000 genomes]
rs74081513	1.00[EUR][1000 genomes]
rs74081517	0.84[EUR][1000 genomes]
rs7955981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7957292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961698	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7966845	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970203	0.82[MEX][hapmap]
rs7974472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv430506	chr12:45003342-45072343	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17650849	C11orf30	trans	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44986800-45015800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:44998200-45024400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:44998800-45018200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:45003200-45014200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:45004800-45020800	Weak transcription	Fetal Brain Female	brain
6	chr12:45004800-45034800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:45004800-45043200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr12:45005000-45023200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:45005000-45031200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:45005000-45044200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr12:45011600-45014400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:45011600-45014400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:45011800-45015800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:45013400-45019000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:45013800-45020200	Weak transcription	Fetal Brain Male	brain

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