Variant report

Variant	rs12269557
Chromosome Location	chr10:98063405-98063406
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98062204..98064987-chr10:98065467..98068204,2	K562	blood:

Variant related genes	Relation type
ENSG00000229418	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10509708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10786277	1.00[CHB][hapmap]
rs10786279	1.00[CHB][hapmap]
rs10882772	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs10882773	1.00[CHB][hapmap]
rs11188697	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11188702	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188705	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188709	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11591467	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs11593073	1.00[CHB][hapmap]
rs11593074	1.00[CHB][hapmap]
rs11593503	1.00[CHB][hapmap]
rs11597348	0.85[CHB][hapmap]
rs11598258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12258764	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs12761473	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12763059	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12766367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12779164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12779203	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12779564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111594	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17111598	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111599	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111603	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17111612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111733	1.00[CHB][hapmap]
rs1815258	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1923707	1.00[CHB][hapmap]
rs1923708	1.00[CHB][hapmap]
rs2146390	0.91[CEU][hapmap]
rs2146394	1.00[CHB][hapmap]
rs2181322	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273891	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap]
rs2861307	0.86[JPT][hapmap]
rs2861572	1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap]
rs34125453	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34128907	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34220987	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34521234	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34943354	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35055142	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35259489	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35388328	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35531390	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35925896	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35933547	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36003947	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789937	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789938	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs3818313	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap]
rs4550161	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4917732	1.00[CHB][hapmap]
rs7073871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077344	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs71482401	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71482402	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484204	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71484205	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72811058	0.81[ASN][1000 genomes]
rs7893551	1.00[CHB][hapmap]
rs7917592	1.00[EUR][1000 genomes];1.00[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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv2761620	chr10:98047045-98089749	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12269557	OPALIN	cis	parietal	SCAN
rs12269557	CHUK	cis	parietal	SCAN
rs12269557	GOT1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98057600-98063800	Enhancers	Fetal Thymus	thymus
2	chr10:98059600-98064200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:98060000-98066200	Weak transcription	Spleen	Spleen
4	chr10:98060000-98068000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:98060600-98065800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr10:98060600-98066000	Weak transcription	Primary B cells from cord blood	blood
7	chr10:98061200-98066200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr10:98061400-98067800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr10:98061800-98066400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr10:98061800-98066400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:98062000-98066200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:98062800-98063800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr10:98063200-98064000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr10:98063200-98065800	Flanking Active TSS	Dnd41	blood
15	chr10:98063200-98067200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:98063400-98064200	Flanking Active TSS	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links