Variant report

Variant	rs6493511
Chromosome Location	chr15:51901605-51901606
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	chr15:51898533..51902972-chr15:51911457..51915866,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1017679	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs10851501	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11070861	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11857716	0.95[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12324531	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12441057	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12708427	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12901452	0.95[CEU][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs12904173	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12904583	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1378892	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1378893	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1378894	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1378895	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1456295	0.95[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1456297	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1471072	0.90[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1551657	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17524750	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17524906	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1840707	0.95[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs1902595	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902596	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2061425	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2252220	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2414112	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2446407	0.95[CEU][hapmap]
rs2606134	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2606136	0.84[ASW][hapmap];0.95[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2606137	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs2606138	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2606139	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2606141	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2606143	1.00[ASW][hapmap];0.90[CEU][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2606145	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2606146	0.95[CEU][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2607110	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2607112	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2607116	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2607117	0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2622768	0.90[EUR][1000 genomes]
rs2622769	0.84[ASW][hapmap];0.95[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2622770	0.95[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs28408214	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34448759	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34532503	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34662965	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34929849	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35011964	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35561856	0.81[EUR][1000 genomes]
rs3751585	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4465557	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4774594	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4775954	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55725532	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56879579	0.86[EUR][1000 genomes]
rs61618680	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6493507	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6493512	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493514	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs716986	0.95[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7180329	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7181921	0.81[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs8025974	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs8026587	0.90[CEU][hapmap];0.82[MEX][hapmap]
rs8027162	0.90[EUR][1000 genomes]
rs8029731	0.90[EUR][1000 genomes]
rs897581	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs956171	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9672605	0.90[EUR][1000 genomes]
rs9806214	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9944266	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv904219	chr15:51851999-51977159	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
3	nsv457139	chr15:51854718-51977159	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
4	nsv569407	chr15:51854718-51977159	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
5	nsv569408	chr15:51867172-51946100	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6493511	ATP8B4	cis	parietal	SCAN
rs6493511	SCG3	cis	parietal	SCAN
rs6493511	BCL2L10	cis	parietal	SCAN
rs6493511	ARPP19	cis	parietal	SCAN
rs6493511	SCG3	cis	cerebellum	SCAN
rs6493511	TMOD2	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51889400-51909400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:51890000-51902000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:51891800-51903800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:51892600-51913000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:51893000-51911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:51893800-51904000	Weak transcription	Fetal Stomach	stomach
7	chr15:51894000-51906000	Weak transcription	Dnd41	blood
8	chr15:51895000-51911600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:51895200-51913000	Weak transcription	HMEC	breast
10	chr15:51896000-51904000	Weak transcription	Lung	lung
11	chr15:51897200-51910800	Weak transcription	A549	lung
12	chr15:51901600-51902200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr15:51901600-51902200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr15:51901600-51902800	Enhancers	Monocytes-CD14+_RO01746	blood

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