Variant report

Variant	rs4242116
Chromosome Location	chr5:42655123-42655124
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42642428..42645184-chr5:42653462..42655294,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10038285	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs10038477	1.00[CEU][hapmap]
rs10041108	0.90[CEU][hapmap]
rs10041130	0.90[CEU][hapmap]
rs10044169	1.00[CEU][hapmap]
rs10050889	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];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10061833	0.88[ASW][hapmap];1.00[CEU][hapmap]
rs10063672	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10074740	0.89[CEU][hapmap]
rs10077296	1.00[CEU][hapmap]
rs10473288	0.88[EUR][1000 genomes]
rs10805665	1.00[CEU][hapmap]
rs10941583	0.90[CEU][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs12513710	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12518067	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521311	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13154178	0.81[GIH][hapmap]
rs1423655	0.90[CEU][hapmap]
rs28551699	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2910860	0.90[CEU][hapmap]
rs2910878	1.00[CEU][hapmap]
rs2972780	0.95[CEU][hapmap]
rs35167647	0.83[ASN][1000 genomes]
rs36109172	0.84[EUR][1000 genomes]
rs3877899	0.85[CEU][hapmap]
rs3884519	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4073475	0.94[EUR][1000 genomes]
rs4073476	0.94[EUR][1000 genomes]
rs4242117	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4242118	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4242119	1.00[CEU][hapmap]
rs4273617	0.88[ASW][hapmap];1.00[CEU][hapmap]
rs4315928	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4357041	0.94[EUR][1000 genomes]
rs4357043	0.95[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4394131	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4518410	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4523006	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4547964	0.93[CEU][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4590183	0.95[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4610468	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4612114	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4637559	0.89[CEU][hapmap]
rs4866948	1.00[CEU][hapmap]
rs56350930	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57624549	0.83[ASN][1000 genomes]
rs59621470	0.83[ASN][1000 genomes]
rs59626862	0.83[ASN][1000 genomes]
rs6179	0.94[ASW][hapmap];0.95[CEU][hapmap]
rs6413428	0.90[CEU][hapmap]
rs6414898	0.90[CEU][hapmap]
rs6451627	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6451628	0.83[ASN][1000 genomes]
rs6451641	0.90[CEU][hapmap]
rs6451643	0.90[CEU][hapmap]
rs6864999	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6873340	0.89[CEU][hapmap]
rs6873545	0.95[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes]
rs6886047	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6897530	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73087466	0.83[ASN][1000 genomes]
rs73087468	0.83[ASN][1000 genomes]
rs73087475	0.83[ASN][1000 genomes]
rs7444761	0.80[CEU][hapmap]
rs7447061	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7701605	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715032	0.90[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes]
rs7729049	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1019648	chr5:42616487-42696943	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv537736	chr5:42616487-42696943	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4242116	CARD6	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42641400-42656000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:42646000-42656600	Weak transcription	Ovary	ovary
3	chr5:42650400-42655800	Weak transcription	NHEK	skin
4	chr5:42650600-42655400	Weak transcription	HMEC	breast
5	chr5:42652600-42655400	Enhancers	Liver	Liver
6	chr5:42652800-42655600	Enhancers	Psoas Muscle	Psoas
7	chr5:42652800-42656800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr5:42653000-42656000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:42653400-42655800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr5:42653600-42655400	Enhancers	Fetal Heart	heart
11	chr5:42654400-42659000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr5:42654600-42655200	Enhancers	Left Ventricle	heart
13	chr5:42654600-42657000	Enhancers	Adipose Nuclei	Adipose
14	chr5:42654800-42657200	Enhancers	Fetal Lung	lung
15	chr5:42655000-42656400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links