Variant report

Variant	rs712328
Chromosome Location	chr14:37240525-37240526
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:37131343..37133633-chr14:37239197..37241870,3	MCF-7	breast:
2	chr14:37239954..37240721-chr14:37325375..37325944,2	MCF-7	breast:
3	chr14:37236787..37238777-chr14:37239104..37242247,3	MCF-7	breast:
4	chr14:37239867..37241978-chr14:37243128..37244915,2	MCF-7	breast:
5	chr14:37238888..37241236-chr14:37420681..37423227,2	MCF-7	breast:
6	chr14:37230759..37233654-chr14:37238626..37240707,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266327	Chromatin interaction
ENSG00000198807	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10134198	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10134532	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10134535	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1325533	0.93[CHB][hapmap];0.84[CHD][hapmap];0.80[YRI][hapmap]
rs1325534	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1325535	1.00[ASW][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1325537	0.93[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1739611	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1739613	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1749926	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1749927	1.00[ASW][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1749928	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1749929	0.93[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1749944	0.93[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1749945	0.93[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1853812	1.00[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2764953	0.93[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2764954	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2764958	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2774037	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2774038	0.93[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2774039	1.00[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs712324	1.00[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712333	0.93[CHB][hapmap];0.89[YRI][hapmap]
rs73264788	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs848090	0.93[CHB][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs848093	1.00[ASW][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs848094	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs848095	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848096	0.93[CHB][hapmap]
rs848098	0.93[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848099	0.91[CHB][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848100	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848101	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848102	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848103	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848104	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848105	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848108	1.00[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs848109	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs848110	0.93[CHB][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848111	1.00[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs848113	0.93[CHB][hapmap];0.89[YRI][hapmap]
rs848114	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848115	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848116	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848117	0.89[YRI][hapmap]
rs848118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848119	1.00[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848122	0.86[CHB][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047290	chr14:36564568-37445157	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1037952	chr14:36670484-37294692	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv542042	chr14:36670484-37294692	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1053685	chr14:36915643-37245920	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs712328	RP11-81F13.2	cis	Esophagus Mucosa	GTEx
rs712328	RP11-81F13.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:37237400-37240600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr14:37237800-37241200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr14:37238000-37242000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr14:37238000-37242000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr14:37238000-37242400	Weak transcription	HMEC	breast
6	chr14:37238000-37242600	Weak transcription	NHEK	skin
7	chr14:37238000-37243000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:37238200-37243000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:37238400-37240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:37238400-37240600	Weak transcription	Esophagus	oesophagus
11	chr14:37238400-37242200	Weak transcription	K562	blood
12	chr14:37238400-37242400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr14:37238400-37243000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr14:37240000-37240800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr14:37240000-37243200	Enhancers	Hela-S3	cervix

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