Variant report

Variant	rs12588797
Chromosome Location	chr14:104300020-104300021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104297034..104301201-chr14:104311770..104316703,7	MCF-7	breast:
2	chr14:104292519..104294178-chr14:104297245..104300059,2	MCF-7	breast:
3	chr14:104281068..104283237-chr14:104297238..104300067,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088808	Chromatin interaction
ENSG00000258735	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10129899	0.88[ASN][1000 genomes]
rs1040813	0.82[JPT][hapmap]
rs11160759	0.82[JPT][hapmap]
rs11160760	0.82[JPT][hapmap]
rs11160762	0.82[JPT][hapmap]
rs1155751	0.83[CHB][hapmap]
rs11623546	0.82[JPT][hapmap]
rs11624184	0.82[JPT][hapmap]
rs11625740	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs11626377	0.82[JPT][hapmap]
rs11628332	0.82[JPT][hapmap]
rs11847468	0.82[JPT][hapmap]
rs1187416	0.82[JPT][hapmap]
rs1187417	1.00[ASW][hapmap];0.88[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12879501	0.82[JPT][hapmap]
rs12879529	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12880821	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs12883337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12885018	0.82[JPT][hapmap]
rs12885509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12886637	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12888002	0.85[EUR][1000 genomes]
rs12889993	0.82[JPT][hapmap]
rs12890354	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12890430	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12890822	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12890837	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12891175	0.82[JPT][hapmap]
rs12891477	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12892189	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12893623	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1475007	0.82[JPT][hapmap]
rs1535097	0.82[JPT][hapmap]
rs1535098	0.82[JPT][hapmap]
rs17791722	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1997913	0.82[JPT][hapmap]
rs2223937	0.82[JPT][hapmap]
rs2295141	0.82[JPT][hapmap]
rs2368560	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2887282	0.82[JPT][hapmap]
rs34596177	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35085624	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35740217	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3742366	0.85[AMR][1000 genomes]
rs3818085	0.82[JPT][hapmap]
rs3861678	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4900594	0.83[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs4900597	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4900600	0.82[JPT][hapmap]
rs4906363	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4906364	0.88[AMR][1000 genomes]
rs4906365	0.88[JPT][hapmap]
rs4906376	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4906377	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4906378	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4906379	0.90[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6575997	0.82[JPT][hapmap]
rs6576006	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6576007	0.90[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6576008	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6576009	0.95[MEX][hapmap]
rs66676135	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66953418	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7142769	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7143885	0.81[AMR][1000 genomes]
rs7156834	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7159810	0.82[JPT][hapmap]
rs722637	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8003653	0.82[JPT][hapmap]
rs8004408	0.82[JPT][hapmap]
rs8005225	0.82[JPT][hapmap]
rs8005594	0.82[JPT][hapmap]
rs8016014	0.82[JPT][hapmap]
rs8017200	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8548	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs876002	0.82[JPT][hapmap]
rs9888591	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[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	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv902313	chr14:104162263-104378087	Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv902318	chr14:104255083-104464809	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
9	nsv902320	chr14:104274294-104308095	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv1838047	chr14:104283104-104359121	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	nsv902321	chr14:104283104-104378087	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12588797	BAG5	cis	multi-tissue	Pritchard
rs12588797	MARK3	cis	cerebellum	SCAN
rs12588797	RP11-73M18.8	cis	Artery Tibial	GTEx
rs12588797	MARK3	cis	parietal	SCAN
rs12588797	C14orf153	cis	parietal	SCAN
rs12588797	ZFYVE21	cis	cerebellum	SCAN
rs12588797	XRCC3	cis	Whole Blood	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104286600-104303400	Weak transcription	Spleen	Spleen
2	chr14:104292000-104312400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr14:104292200-104303800	Weak transcription	HepG2	liver
4	chr14:104292800-104309000	Weak transcription	Fetal Intestine Small	intestine
5	chr14:104295200-104303400	Weak transcription	Ovary	ovary
6	chr14:104295200-104303600	Weak transcription	Fetal Lung	lung
7	chr14:104295200-104306000	Weak transcription	HMEC	breast
8	chr14:104295200-104309000	Weak transcription	Fetal Stomach	stomach
9	chr14:104295200-104311600	Weak transcription	Liver	Liver
10	chr14:104295200-104312200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr14:104295200-104312400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr14:104295200-104312600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr14:104295200-104312600	Weak transcription	Small Intestine	intestine
14	chr14:104298200-104300600	Enhancers	Right Ventricle	heart
15	chr14:104298600-104300800	Enhancers	Gastric	stomach
16	chr14:104298800-104300200	Enhancers	Left Ventricle	heart
17	chr14:104298800-104301200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr14:104299000-104305800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr14:104299000-104306000	Weak transcription	NHEK	skin
20	chr14:104299000-104312200	Weak transcription	Hela-S3	cervix
21	chr14:104299600-104300600	Enhancers	Pancreas	Pancrea
22	chr14:104300000-104300400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr14:104300000-104300400	Enhancers	Fetal Heart	heart
24	chr14:104300000-104300600	Enhancers	Right Atrium	heart
25	chr14:104300000-104301400	Weak transcription	Lung	lung

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