Variant report

Variant	rs12677519
Chromosome Location	chr8:95690579-95690580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:95690436..95692309-chr8:95699659..95701604,2	MCF-7	breast:
2	chr8:95688255..95691100-chr8:95707939..95710174,2	MCF-7	breast:
3	chr8:95651374..95653284-chr8:95688845..95691159,2	MCF-7	breast:
4	chr8:95654087..95655784-chr8:95690231..95692944,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104413	Chromatin interaction
ENSG00000261437	Chromatin interaction
ENSG00000241003	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10091213	0.86[ASN][1000 genomes]
rs1046155	0.86[ASN][1000 genomes]
rs1046163	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10956925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11785	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12542239	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12543234	0.86[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.93[ASN][1000 genomes]
rs12543253	0.99[ASN][1000 genomes]
rs12543258	0.93[ASN][1000 genomes]
rs12543404	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12543514	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12544778	0.98[ASN][1000 genomes]
rs12545296	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12545684	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12545776	0.89[ASN][1000 genomes]
rs12546263	0.89[ASN][1000 genomes]
rs12546282	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs12548165	0.91[ASN][1000 genomes]
rs12550043	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12675372	0.86[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.92[ASN][1000 genomes]
rs12676890	0.92[ASN][1000 genomes]
rs12676908	0.92[ASN][1000 genomes]
rs12677807	0.92[ASN][1000 genomes]
rs12677830	0.92[ASN][1000 genomes]
rs12678311	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12678709	0.92[ASN][1000 genomes]
rs12678729	0.92[ASN][1000 genomes]
rs13254184	0.85[ASN][1000 genomes]
rs13266255	0.85[ASN][1000 genomes]
rs1365203	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1365205	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[ASN][1000 genomes]
rs1549466	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs15710	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs15726	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs17717161	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2033074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033075	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2052718	0.90[ASN][1000 genomes]
rs2052719	0.93[ASN][1000 genomes]
rs2052720	0.93[ASN][1000 genomes]
rs2052721	0.93[ASN][1000 genomes]
rs2068005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241504	0.97[ASN][1000 genomes]
rs2241505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288260	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2303453	0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2554396	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2554397	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2554400	0.84[YRI][hapmap]
rs2722874	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2722876	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2722883	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2722884	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs34733016	0.86[ASN][1000 genomes]
rs3864655	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.93[ASN][1000 genomes]
rs4008177	0.85[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs4348460	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4348461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4481558	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4639480	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.87[ASN][1000 genomes]
rs55865498	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55890917	0.92[ASN][1000 genomes]
rs57653937	0.89[ASN][1000 genomes]
rs58422141	0.91[ASN][1000 genomes]
rs59515090	0.92[ASN][1000 genomes]
rs59557867	0.82[ASN][1000 genomes]
rs60573557	0.89[ASN][1000 genomes]
rs62523459	0.80[ASN][1000 genomes]
rs6471457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471460	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6471461	0.88[ASN][1000 genomes]
rs6471462	0.89[ASN][1000 genomes]
rs6471464	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6471465	0.86[ASN][1000 genomes]
rs6471466	0.86[ASN][1000 genomes]
rs6471467	0.86[ASN][1000 genomes]
rs6471468	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6471470	0.85[ASN][1000 genomes]
rs6471471	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6471472	0.85[ASN][1000 genomes]
rs6471473	0.83[ASN][1000 genomes]
rs6471474	0.84[ASN][1000 genomes]
rs6471475	0.85[ASN][1000 genomes]
rs66477120	0.99[ASN][1000 genomes]
rs66850135	0.99[ASN][1000 genomes]
rs67900173	0.86[ASN][1000 genomes]
rs6988635	0.91[JPT][hapmap]
rs7010722	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7016360	0.86[ASN][1000 genomes]
rs7017752	0.89[ASN][1000 genomes]
rs7017996	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs72676924	0.98[ASN][1000 genomes]
rs72676929	0.93[ASN][1000 genomes]
rs72676935	0.92[ASN][1000 genomes]
rs7387164	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7388010	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7461991	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7462846	0.86[ASN][1000 genomes]
rs7464856	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7812489	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7813216	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs7813657	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7814238	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.91[ASN][1000 genomes]
rs7814803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7815719	0.88[ASN][1000 genomes]
rs7816188	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7816645	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7820441	0.91[ASN][1000 genomes]
rs7823050	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7824332	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7829467	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7832022	0.91[ASN][1000 genomes]
rs7832771	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7833299	0.80[ASN][1000 genomes]
rs7833363	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7836949	0.91[ASN][1000 genomes]
rs7840284	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7842246	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7842400	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7842716	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9643347	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12677519	PLEKHF2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95655600-95701200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:95656400-95701000	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr8:95656400-95713000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr8:95656600-95699200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr8:95656600-95701200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr8:95656600-95701600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr8:95656600-95703200	Weak transcription	Stomach Mucosa	stomach
8	chr8:95657200-95701200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr8:95657600-95699400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr8:95660600-95698000	Weak transcription	Fetal Stomach	stomach
11	chr8:95662600-95694600	Weak transcription	Lung	lung
12	chr8:95664600-95692600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr8:95668400-95693600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr8:95670800-95698800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:95670800-95703000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:95679600-95699000	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr8:95680600-95694200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr8:95680600-95718400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr8:95681400-95704400	Weak transcription	Gastric	stomach
20	chr8:95682400-95690800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr8:95686800-95697000	Weak transcription	Esophagus	oesophagus
22	chr8:95688200-95690600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
23	chr8:95688600-95693600	Weak transcription	Fetal Intestine Large	intestine
24	chr8:95689400-95695200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr8:95689800-95690600	Strong transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr8:95689800-95691800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr8:95689800-95692400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr8:95690000-95691000	Strong transcription	Colonic Mucosa	Colon
29	chr8:95690200-95691000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr8:95690200-95691800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr8:95690200-95691800	Enhancers	HSMMtube	muscle
32	chr8:95690200-95692000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr8:95690200-95693000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr8:95690200-95698600	Strong transcription	Fetal Intestine Small	intestine
35	chr8:95690200-95701000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr8:95690200-95701200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr8:95690400-95690800	Enhancers	Left Ventricle	heart
38	chr8:95690400-95690800	Enhancers	Right Atrium	heart
39	chr8:95690400-95690800	Flanking Active TSS	HepG2	liver
40	chr8:95690400-95690800	Genic enhancers	HMEC	breast
41	chr8:95690400-95690800	Genic enhancers	NHEK	skin
42	chr8:95690400-95691000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr8:95690400-95691000	Flanking Active TSS	Fetal Heart	heart
44	chr8:95690400-95691800	Strong transcription	Pancreas	Pancrea
45	chr8:95690400-95692400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr8:95690400-95693000	Strong transcription	Placenta	Placenta

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