Variant report

Variant	rs1435253
Chromosome Location	chr9:101055154-101055155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101053777..101056513-chr9:101062156..101064768,2	K562	blood:
2	chr9:101053633..101055705-chr9:101074383..101076879,2	K562	blood:
3	chr9:101051613..101053576-chr9:101054948..101058206,3	K562	blood:
4	chr9:101049774..101053402-chr9:101054314..101056733,3	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10115971	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10123643	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10124977	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10760210	1.00[JPT][hapmap]
rs10760216	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10760218	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10818640	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10818648	0.87[AMR][1000 genomes]
rs10818656	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10818662	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs10818667	1.00[JPT][hapmap]
rs10818672	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10818676	0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10818677	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10818678	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10818689	0.89[AMR][1000 genomes]
rs10818690	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10818691	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10818692	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10818693	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10818739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985517	1.00[JPT][hapmap]
rs10985583	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10985634	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10985641	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985642	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985653	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985669	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985680	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985689	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985711	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985720	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985743	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10985745	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10985757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10985765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10985780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10985808	0.85[CHB][hapmap]
rs10985817	0.85[CHB][hapmap]
rs10985819	0.85[CHB][hapmap]
rs10985825	0.85[CHB][hapmap]
rs10985826	0.85[CHB][hapmap]
rs12237988	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12338195	1.00[YRI][hapmap]
rs1435257	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1573025	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17766883	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17766913	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1935389	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2275709	1.00[YRI][hapmap]
rs2304389	0.85[CHB][hapmap]
rs2304390	0.85[CHB][hapmap]
rs3780444	0.85[CHB][hapmap]
rs3780445	0.85[CHB][hapmap]
rs3780447	1.00[MKK][hapmap]
rs4379551	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4742721	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4742722	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4743187	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4743188	1.00[JPT][hapmap]
rs4743192	0.89[AMR][1000 genomes]
rs4743194	1.00[JPT][hapmap]
rs5010004	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs56262782	0.82[ASN][1000 genomes]
rs62574277	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62574288	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62574300	0.85[ASN][1000 genomes]
rs6478631	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7042576	1.00[JPT][hapmap]
rs7045158	1.00[JPT][hapmap]
rs7853442	1.00[JPT][hapmap]
rs7853847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs7856392	0.85[CHB][hapmap]
rs7859655	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7867465	0.85[CHB][hapmap]
rs7867834	0.85[CHB][hapmap]
rs7868451	1.00[JPT][hapmap]
rs7869257	0.85[CHB][hapmap]
rs7869364	0.85[CHB][hapmap]
rs7873849	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7874856	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs879368	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs879369	1.00[JPT][hapmap]
rs9696283	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9802650	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv831664	chr9:101024862-101205637	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv519818	chr9:101024887-101092316	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1435253	ZNF367	cis	parietal	SCAN
rs1435253	C9orf21	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101049000-101062800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:101049800-101060600	Weak transcription	Brain Angular Gyrus	brain
3	chr9:101050400-101055400	Enhancers	Placenta	Placenta
4	chr9:101050600-101064600	Weak transcription	Fetal Brain Female	brain
5	chr9:101051200-101055400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:101052400-101065800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:101053000-101056000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:101053800-101055400	Strong transcription	Brain Germinal Matrix	brain
9	chr9:101054400-101056400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:101054600-101055400	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr9:101054600-101063600	Weak transcription	K562	blood

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