Variant report

Variant	rs42346
Chromosome Location	chr8:90829057-90829058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:90827148..90830083-chr8:90913330..90915459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1003843	0.82[GIH][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs10095743	0.86[AMR][1000 genomes]
rs10112852	0.86[AMR][1000 genomes]
rs13252917	0.86[AMR][1000 genomes]
rs13259882	0.86[AMR][1000 genomes]
rs13274635	0.85[CEU][hapmap]
rs218905	0.82[AMR][1000 genomes]
rs218907	0.85[AMR][1000 genomes]
rs218908	0.85[AMR][1000 genomes]
rs218909	0.85[AMR][1000 genomes]
rs218913	0.82[GIH][hapmap];0.85[AMR][1000 genomes]
rs218914	0.85[AMR][1000 genomes]
rs218925	0.87[AMR][1000 genomes]
rs218929	0.82[GIH][hapmap];0.87[AMR][1000 genomes]
rs218932	0.85[AMR][1000 genomes]
rs218934	0.85[AMR][1000 genomes]
rs218936	0.88[AMR][1000 genomes]
rs218938	0.85[CEU][hapmap]
rs2644021	0.86[AMR][1000 genomes]
rs2644033	0.87[AMR][1000 genomes]
rs2735870	0.85[AMR][1000 genomes]
rs2735871	0.87[AMR][1000 genomes]
rs2735873	0.87[AMR][1000 genomes]
rs2735878	0.86[AMR][1000 genomes]
rs2735882	0.86[AMR][1000 genomes]
rs28144	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2975240	0.90[EUR][1000 genomes]
rs367640	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs368812	0.92[EUR][1000 genomes]
rs369771	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs370282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376110	0.93[EUR][1000 genomes]
rs376962	0.86[JPT][hapmap]
rs377897	0.86[JPT][hapmap]
rs380425	0.81[JPT][hapmap]
rs381456	0.86[JPT][hapmap]
rs383592	0.92[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs385524	0.87[AMR][1000 genomes]
rs388866	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs390536	0.86[JPT][hapmap]
rs394108	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs39500	1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs39503	0.84[GIH][hapmap];0.83[MEX][hapmap];0.89[AMR][1000 genomes]
rs39504	0.89[AMR][1000 genomes]
rs39505	0.89[AMR][1000 genomes]
rs39506	0.84[GIH][hapmap];0.83[MEX][hapmap];0.89[AMR][1000 genomes]
rs39509	0.92[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs39515	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs39516	0.92[EUR][1000 genomes]
rs397540	0.85[CEU][hapmap]
rs39761	1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs39763	0.85[CEU][hapmap]
rs39766	0.85[CEU][hapmap]
rs39767	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs39768	0.91[EUR][1000 genomes]
rs39769	0.92[EUR][1000 genomes]
rs400411	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs402434	0.92[EUR][1000 genomes]
rs40247	0.89[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs40250	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs402886	1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs40379	0.85[CEU][hapmap]
rs40380	0.82[CEU][hapmap]
rs40381	0.84[EUR][1000 genomes]
rs40382	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40452	1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs40453	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs40454	0.82[CEU][hapmap]
rs40457	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40459	0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs40545	0.89[AMR][1000 genomes]
rs40547	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405734	0.87[AMR][1000 genomes]
rs40635	0.85[CEU][hapmap]
rs40636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs40637	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40638	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40639	0.89[EUR][1000 genomes]
rs410663	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs411279	0.89[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs411310	0.85[CEU][hapmap]
rs416324	0.92[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs418634	0.81[JPT][hapmap]
rs419754	0.87[AMR][1000 genomes]
rs419890	0.81[ASN][1000 genomes]
rs421411	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs42186	0.81[ASN][1000 genomes]
rs422559	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs42343	0.85[CEU][hapmap]
rs42344	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs42345	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs42480	0.85[CEU][hapmap]
rs42481	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs42490	0.82[GIH][hapmap]
rs425140	0.81[JPT][hapmap]
rs427854	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs428484	0.85[CEU][hapmap]
rs43134	0.84[GIH][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs43135	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs43225	1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs43226	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs43227	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs43228	0.93[EUR][1000 genomes]
rs432457	0.86[JPT][hapmap]
rs434264	0.85[CEU][hapmap]
rs435600	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs441548	0.81[EUR][1000 genomes]
rs445172	0.92[EUR][1000 genomes]
rs445675	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs447611	0.92[EUR][1000 genomes]
rs447618	0.84[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs447989	0.81[JPT][hapmap]
rs450332	0.84[CEU][hapmap]
rs452694	0.92[EUR][1000 genomes]
rs453266	0.92[EUR][1000 genomes]
rs454561	0.92[EUR][1000 genomes]
rs465	0.85[AMR][1000 genomes]
rs51331	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6470366	0.86[AMR][1000 genomes]
rs6992985	0.86[AMR][1000 genomes]
rs6993133	0.86[AMR][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	nsv972243	chr8:90823430-90834708	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs42346	RIPK2	cis	cerebellum	SCAN
rs42346	RIPK2	Cis_1M	lymphoblastoid	RTeQTL
rs42346	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs42346	RP11-37B2.1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90824000-90836600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:90825400-90829400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr8:90826800-90829200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:90827800-90829200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:90828000-90845800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr8:90828600-90829400	Enhancers	Osteobl	bone
7	chr8:90828800-90829400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr8:90828800-90829400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr8:90828800-90830600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr8:90829000-90829200	Enhancers	Aorta	Aorta
11	chr8:90829000-90829200	Enhancers	HMEC	breast
12	chr8:90829000-90829200	Enhancers	NHDF-Ad	bronchial
13	chr8:90829000-90829400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:90829000-90829400	Enhancers	NH-A	brain
15	chr8:90829000-90829600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr8:90829000-90829800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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