Variant report

Variant	rs40459
Chromosome Location	chr8:90846226-90846227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153928343..153930810-chr8:90845808..90848291,2	MCF-7	breast:
2	chr8:90845301..90847765-chr8:90850348..90853325,2	MCF-7	breast:
3	chr8:90838601..90840941-chr8:90843850..90846321,2	MCF-7	breast:
4	chr8:90843753..90846365-chr8:90914514..90916042,2	MCF-7	breast:
5	chr8:90844734..90847246-chr8:90847760..90849982,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164823	Chromatin interaction
ENSG00000160741	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1003843	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs10112852	0.81[CEU][hapmap]
rs218902	0.81[CEU][hapmap]
rs2189025	0.81[ASN][1000 genomes]
rs218907	0.81[CEU][hapmap]
rs218908	0.81[CEU][hapmap]
rs218913	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs218929	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs366867	0.89[ASN][1000 genomes]
rs367640	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs370282	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs374957	0.92[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs376962	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs377897	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs379015	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs380425	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs381456	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs383592	0.83[GIH][hapmap]
rs386587	0.94[ASN][1000 genomes]
rs388866	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs390536	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[ASN][1000 genomes]
rs39499	0.81[CEU][hapmap]
rs39500	0.81[CEU][hapmap]
rs39503	0.89[GIH][hapmap]
rs39506	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs39519	0.92[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs39761	0.81[CEU][hapmap]
rs39771	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs39772	0.94[EUR][1000 genomes]
rs40250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs402886	0.81[CEU][hapmap]
rs40382	0.83[ASN][1000 genomes]
rs40452	0.81[CEU][hapmap]
rs40453	0.84[GIH][hapmap]
rs40547	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs40638	0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs410663	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs411279	0.84[GIH][hapmap]
rs416324	0.84[GIH][hapmap]
rs418634	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs419890	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42186	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42346	0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs42481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42490	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs425140	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[ASN][1000 genomes]
rs425312	0.93[EUR][1000 genomes]
rs426240	0.94[EUR][1000 genomes]
rs427854	0.91[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs43134	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs43135	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs43136	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs43225	0.81[CEU][hapmap]
rs43229	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs432457	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[ASN][1000 genomes]
rs438485	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs447618	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs447989	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv520356	chr8:90823687-90857989	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2761448	chr8:90837630-90853986	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs40459	RIPK2	cis	cerebellum	SCAN
rs40459	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs40459	OSGIN2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90837000-90847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr8:90839200-90848400	Weak transcription	Osteobl	bone
3	chr8:90840000-90847400	Weak transcription	A549	lung
4	chr8:90845000-90847600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr8:90845800-90846600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr8:90845800-90846600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr8:90845800-90848000	Flanking Active TSS	GM12878-XiMat	blood
8	chr8:90845800-90850200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr8:90846000-90846800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:90846000-90850400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr8:90846000-90850600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr8:90846200-90846600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr8:90846200-90846600	Enhancers	NHDF-Ad	bronchial
14	chr8:90846200-90847200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr8:90846200-90848000	Enhancers	Primary hematopoietic stem cells	blood
16	chr8:90846200-90848200	Weak transcription	NHLF	lung
17	chr8:90846200-90848600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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