Variant report

Variant	rs12518067
Chromosome Location	chr5:42656600-42656601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:42652279..42654672-chr5:42655371..42657991,3	K562	blood:
2	chr5:42228294..42229001-chr5:42656539..42657726,4	MCF-7	breast:
3	chr5:42652873..42654672-chr5:42656285..42657991,2	K562	blood:
4	chr5:42514982..42515546-chr5:42656463..42657052,2	MCF-7	breast:
5	chr5:41856471..41857410-chr5:42656558..42657380,2	MCF-7	breast:
6	chr5:42423150..42423979-chr5:42656079..42656931,2	MCF-7	breast:
7	chr5:42583117..42583623-chr5:42656473..42657357,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112964	Chromatin interaction

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]
rs12521311	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13154178	0.82[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]
rs4242116	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]
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
rs12518067	CARD6	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42646000-42656600	Weak transcription	Ovary	ovary
2	chr5:42652800-42656800	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr5:42654400-42659000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr5:42654600-42657000	Enhancers	Adipose Nuclei	Adipose
5	chr5:42654800-42657200	Enhancers	Fetal Lung	lung
6	chr5:42655400-42657000	Enhancers	Fetal Kidney	kidney
7	chr5:42655400-42658400	Weak transcription	Liver	Liver
8	chr5:42655600-42656600	Weak transcription	Psoas Muscle	Psoas
9	chr5:42655800-42656800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:42656000-42656800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:42656000-42657000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:42656200-42656600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:42656200-42656600	Enhancers	NH-A	brain
14	chr5:42656200-42656800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr5:42656200-42656800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr5:42656200-42656800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr5:42656200-42656800	Active TSS	Right Atrium	heart
18	chr5:42656200-42656800	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr5:42656200-42656800	Enhancers	HSMM	muscle
20	chr5:42656200-42657000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:42656200-42657000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:42656200-42657400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr5:42656400-42656800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:42656400-42656800	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr5:42656400-42656800	Flanking Active TSS	NHEK	skin
26	chr5:42656400-42656800	Enhancers	NHLF	lung
27	chr5:42656400-42657000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:42656400-42657000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:42656400-42657000	Flanking Active TSS	HMEC	breast
30	chr5:42656400-42657200	Enhancers	Fetal Heart	heart
31	chr5:42656600-42656800	Flanking Active TSS	Ovary	ovary
32	chr5:42656600-42656800	Enhancers	Psoas Muscle	Psoas
33	chr5:42656600-42657000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:42656600-42657000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr5:42656600-42657000	Active TSS	Stomach Smooth Muscle	stomach

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