Variant report

Variant	rs4590183
Chromosome Location	chr5:42626206-42626207
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	chr5:42626104..42628276-chr5:42639236..42641791,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10038285	0.95[CEU][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs10038477	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs10041108	0.85[CEU][hapmap]
rs10041130	0.85[CEU][hapmap]
rs10044169	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs10050889	0.95[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs10061833	0.95[CEU][hapmap]
rs10063672	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074740	0.84[CEU][hapmap]
rs10077296	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs10473288	0.83[EUR][1000 genomes]
rs10805665	0.95[CEU][hapmap]
rs10941583	0.85[CEU][hapmap]
rs12513710	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12518067	0.95[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12521311	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1423655	0.85[CEU][hapmap]
rs28551699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910860	0.85[CEU][hapmap]
rs2910878	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs2972780	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs36109172	0.84[EUR][1000 genomes]
rs3877899	0.81[CEU][hapmap]
rs3884519	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073475	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4073476	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4146624	0.83[CHD][hapmap]
rs4242116	0.95[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4242117	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4242118	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4242119	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs4273617	0.95[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs4315928	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4357041	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4357043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4394131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518410	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4523006	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547964	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4610468	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4612114	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4637559	0.84[CEU][hapmap]
rs4866948	0.95[CEU][hapmap]
rs56350930	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6179	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs6413428	0.85[CEU][hapmap]
rs6414898	0.85[CEU][hapmap]
rs6451627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451641	0.85[CEU][hapmap]
rs6451643	0.85[CEU][hapmap]
rs6864999	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6873340	0.84[CEU][hapmap]
rs6873545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6886047	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6897530	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7447061	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7701605	0.95[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7715032	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1027023	chr5:42610250-42654999	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	esv1810677	chr5:42623245-42630968	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv1808812	chr5:42626206-42630968	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv511284	chr5:42626206-42631264	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4590183	CARD6	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42610800-42626800	Weak transcription	Pancreas	Pancrea
2	chr5:42621800-42629000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:42622600-42626800	Weak transcription	Ovary	ovary
4	chr5:42622600-42626800	Weak transcription	Right Ventricle	heart
5	chr5:42622600-42627800	Weak transcription	Left Ventricle	heart
6	chr5:42622600-42628800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:42622800-42631200	Weak transcription	Adipose Nuclei	Adipose
8	chr5:42623000-42626600	Weak transcription	Fetal Heart	heart
9	chr5:42623000-42631400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:42623000-42644400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:42623200-42631400	Weak transcription	Right Atrium	heart
12	chr5:42623800-42632000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:42624000-42626400	Weak transcription	Psoas Muscle	Psoas
14	chr5:42624400-42629400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr5:42624600-42626800	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:42624600-42648000	Weak transcription	Fetal Lung	lung
17	chr5:42626200-42626600	ZNF genes & repeats	Aorta	Aorta
18	chr5:42626200-42626800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:42626200-42627200	Enhancers	Liver	Liver
20	chr5:42626200-42628400	Enhancers	Skeletal Muscle Female	skeletal muscle

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