Variant report

Variant	rs9768604
Chromosome Location	chr7:33262190-33262191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10225173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10228486	0.91[ASN][1000 genomes]
rs10251775	1.00[CHB][hapmap]
rs10254116	0.94[ASW][hapmap];0.91[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs10260015	0.81[EUR][1000 genomes]
rs10262453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10262890	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10271927	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10272438	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12155002	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12530700	1.00[CHB][hapmap]
rs12534242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536300	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs12537875	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12538649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1345306	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1420152	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1420154	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1590140	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17396870	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17724206	1.00[CHB][hapmap]
rs1978333	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28435377	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28789535	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3843532	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs4720113	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4720114	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4723276	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6946608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6947352	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979640	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7785463	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7789007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029220	chr7:32921484-33262190	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv830943	chr7:33167106-33352759	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv606610	chr7:33218763-33486316	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1016416	chr7:33241443-33559477	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	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
rs9768604	C7orf41	cis	cerebellum	SCAN
rs9768604	NPSR1	cis	parietal	SCAN
rs9768604	BBS9	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33251400-33265400	Weak transcription	Gastric	stomach
2	chr7:33252400-33263200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr7:33252800-33266400	Weak transcription	Left Ventricle	heart
4	chr7:33253600-33263400	Weak transcription	Primary T cells from cord blood	blood
5	chr7:33261600-33262400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:33262000-33262200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:33262000-33262200	Enhancers	Ovary	ovary
8	chr7:33262000-33262200	Enhancers	HepG2	liver

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