Variant report

Variant	rs4961159
Chromosome Location	chr8:90703905-90703906
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:90701508..90704091-chr8:90704725..90706436,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10956226	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13278061	0.83[EUR][1000 genomes]
rs1603288	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs160408	0.82[EUR][1000 genomes]
rs160409	0.80[EUR][1000 genomes]
rs160410	0.82[EUR][1000 genomes]
rs160418	0.81[EUR][1000 genomes]
rs160419	1.00[JPT][hapmap]
rs160423	0.82[EUR][1000 genomes]
rs160424	0.80[EUR][1000 genomes]
rs160427	0.81[EUR][1000 genomes]
rs160429	0.83[EUR][1000 genomes]
rs160437	0.84[EUR][1000 genomes]
rs160445	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs160448	0.80[EUR][1000 genomes]
rs160449	0.80[EUR][1000 genomes]
rs160450	0.80[EUR][1000 genomes]
rs160451	0.80[EUR][1000 genomes]
rs2132348	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs216986	0.82[EUR][1000 genomes]
rs216989	0.81[EUR][1000 genomes]
rs216990	0.88[EUR][1000 genomes]
rs218884	0.80[EUR][1000 genomes]
rs218886	0.83[EUR][1000 genomes]
rs218888	0.83[EUR][1000 genomes]
rs218889	0.83[EUR][1000 genomes]
rs218892	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs218896	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs218898	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs218904	0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs218917	0.83[MEX][hapmap];0.85[EUR][1000 genomes]
rs218920	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs218938	1.00[CHD][hapmap]
rs218943	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs218945	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs218949	0.88[EUR][1000 genomes]
rs218950	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs218951	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs218952	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2735886	0.82[EUR][1000 genomes]
rs39770	1.00[CHB][hapmap]
rs400077	1.00[CHB][hapmap]
rs419004	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6999425	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7003919	0.85[EUR][1000 genomes]
rs7018416	0.82[YRI][hapmap]
rs7828553	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv465735	chr8:89760311-90729507	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv611714	chr8:89760311-90729507	Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv870380	chr8:90546585-90720182	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1026523	chr8:90558935-90722580	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv831389	chr8:90575517-90753120	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1017263	chr8:90605445-90722580	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1031578	chr8:90670102-90757821	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3340425	chr8:90686312-90722629	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv891180	chr8:90697810-90802491	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4961159	RIPK2	cis	cerebellum	SCAN
rs4961159	CNGB3	cis	parietal	SCAN
rs4961159	RIPK2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90693200-90715600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:90703800-90704400	Enhancers	NH-A	brain

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