Variant report

Variant	rs12899138
Chromosome Location	chr15:59666246-59666247
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59663366-59667532	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59518511..59521491-chr15:59664302..59666468,2	MCF-7	breast:

Variant related genes	Relation type
MYO1E	TF binding region
ENSG00000157483	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10851653	0.99[ASN][1000 genomes]
rs11071432	1.00[ASN][1000 genomes]
rs11071433	0.99[ASN][1000 genomes]
rs11630796	0.85[ASN][1000 genomes]
rs11631146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11631451	0.97[ASN][1000 genomes]
rs11632346	0.94[ASN][1000 genomes]
rs11634604	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11635849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637840	0.85[ASN][1000 genomes]
rs11639217	0.96[ASN][1000 genomes]
rs11854356	0.93[ASN][1000 genomes]
rs11854697	0.85[ASN][1000 genomes]
rs11855765	0.97[ASN][1000 genomes]
rs11858264	0.88[ASN][1000 genomes]
rs11858313	0.88[ASN][1000 genomes]
rs12050546	0.97[ASN][1000 genomes]
rs12441388	0.97[ASN][1000 genomes]
rs12442217	0.92[ASN][1000 genomes]
rs12593355	0.88[ASN][1000 genomes]
rs12905793	0.85[ASN][1000 genomes]
rs12911676	0.90[ASN][1000 genomes]
rs1580426	0.84[ASN][1000 genomes]
rs16941369	0.95[ASN][1000 genomes]
rs17236585	0.88[ASN][1000 genomes]
rs17302351	0.94[ASN][1000 genomes]
rs2170895	0.85[ASN][1000 genomes]
rs28363891	0.86[ASN][1000 genomes]
rs28380572	0.85[ASN][1000 genomes]
rs28572451	0.87[ASN][1000 genomes]
rs4774327	0.97[ASN][1000 genomes]
rs4775158	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs59107240	0.85[ASN][1000 genomes]
rs61692274	0.84[ASN][1000 genomes]
rs62012550	0.92[ASN][1000 genomes]
rs6494101	0.95[ASN][1000 genomes]
rs6494102	0.95[ASN][1000 genomes]
rs6494105	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66595425	0.92[ASN][1000 genomes]
rs66991143	0.85[ASN][1000 genomes]
rs67498027	0.85[ASN][1000 genomes]
rs7162228	0.88[ASN][1000 genomes]
rs7168074	0.89[ASN][1000 genomes]
rs7173362	0.99[ASN][1000 genomes]
rs7178041	0.99[ASN][1000 genomes]
rs8024396	0.90[ASN][1000 genomes]
rs8024879	0.90[ASN][1000 genomes]
rs8024906	0.90[ASN][1000 genomes]
rs8025242	0.88[ASN][1000 genomes]
rs8025360	0.89[ASN][1000 genomes]
rs8031423	0.97[ASN][1000 genomes]
rs8039327	0.85[ASN][1000 genomes]
rs8041804	0.85[ASN][1000 genomes]
rs965929	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv457175	chr15:59609753-59681214	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv569603	chr15:59609753-59681214	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv471246	chr15:59610743-59681214	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv904274	chr15:59623576-59689378	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv904275	chr15:59648633-59726610	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
8	nsv904276	chr15:59648633-59743010	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59662600-59666600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr15:59662600-59667600	Active TSS	GM12878-XiMat	blood
3	chr15:59663800-59666400	Active TSS	A549	lung
4	chr15:59665400-59666800	Weak transcription	Stomach Mucosa	stomach
5	chr15:59665400-59667000	Enhancers	Small Intestine	intestine
6	chr15:59665400-59667400	Weak transcription	Gastric	stomach
7	chr15:59665600-59666400	Weak transcription	Fetal Heart	heart
8	chr15:59665600-59666400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr15:59665800-59666400	Enhancers	HUVEC	blood vessel
10	chr15:59665800-59668800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr15:59665800-59674000	Weak transcription	Fetal Kidney	kidney
12	chr15:59665800-59675800	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:59665800-59678400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:59665800-59680200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:59665800-59691800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:59666000-59666400	Flanking Active TSS	Liver	Liver
17	chr15:59666000-59666600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr15:59666000-59667000	Weak transcription	Aorta	Aorta
19	chr15:59666000-59667000	Enhancers	HepG2	liver
20	chr15:59666000-59667400	Enhancers	Primary B cells from cord blood	blood
21	chr15:59666000-59672600	Weak transcription	Placenta	Placenta
22	chr15:59666000-59674400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:59666000-59674800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:59666000-59676400	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:59666000-59677000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:59666000-59678400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:59666000-59678400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:59666000-59678800	Weak transcription	Fetal Lung	lung
29	chr15:59666000-59680800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:59666200-59666400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr15:59666200-59666400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:59666200-59666400	Flanking Active TSS	Hela-S3	cervix
33	chr15:59666200-59666600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:59666200-59667000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:59666200-59667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:59666200-59667400	Enhancers	Fetal Intestine Large	intestine
37	chr15:59666200-59671200	Weak transcription	Fetal Intestine Small	intestine
38	chr15:59666200-59671800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:59666200-59673200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:59666200-59674000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:59666200-59680400	Weak transcription	Fetal Stomach	stomach
42	chr15:59666200-59680600	Weak transcription	NHEK	skin
43	chr15:59666200-59681800	Weak transcription	Ovary	ovary

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