Variant report

Variant	rs954152
Chromosome Location	chr15:39891201-39891202
allele	A/G
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	chr15:39891127-39891639	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:39889685-39892072	A549	lung:	n/a	n/a
3	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
4	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
5	POLR2A	chr15:39888328-39893316	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr15:39871636-39892218	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr15:39871327-39893495	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr15:39887322-39891967	MCF-7	breast:	n/a	n/a
9	POLR2A	chr15:39870574-39892778	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr15:39871778-39892493	ProgFib	skin:	n/a	n/a
11	POLR2A	chr15:39871484-39892179	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr15:39889532-39892326	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr15:39871294-39893132	IMR90	lung:	n/a	n/a
14	POLR2A	chr15:39891160-39891686	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr15:39889706-39892219	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr15:39889587-39891348	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39161856..39164781-chr15:39889868..39892142,2	MCF-7	breast:
2	chr15:39890163..39892186-chr15:39958834..39961393,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259279	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1038097	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1051442	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10520141	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10520143	0.87[EUR][1000 genomes]
rs10520146	0.80[EUR][1000 genomes]
rs1382443	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1382444	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16969487	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16969491	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16969547	0.81[EUR][1000 genomes]
rs17632916	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633107	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17633210	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17705806	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17706083	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17706179	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1813493	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1988082	0.82[EUR][1000 genomes]
rs1988555	0.85[EUR][1000 genomes]
rs2228263	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2411316	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2618156	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2618160	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618161	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2618164	0.93[EUR][1000 genomes]
rs2618165	0.93[EUR][1000 genomes]
rs2618167	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2664123	0.92[EUR][1000 genomes]
rs2664136	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664137	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2664138	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664140	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664142	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377784	0.92[EUR][1000 genomes]
rs28549326	0.92[EUR][1000 genomes]
rs28619289	0.92[EUR][1000 genomes]
rs28653011	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34878675	0.87[EUR][1000 genomes]
rs41315060	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4415979	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4503768	0.85[EUR][1000 genomes]
rs45461294	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923835	0.85[EUR][1000 genomes]
rs58188999	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59578395	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59628570	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6492905	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74008647	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74008648	0.92[EUR][1000 genomes]
rs880270	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9972350	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39887000-39891600	Weak transcription	Fetal Brain Male	brain
2	chr15:39888400-39891400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:39888400-39891400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:39888400-39891600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:39888400-39891600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:39888400-39891600	Weak transcription	Fetal Stomach	stomach
7	chr15:39888400-39891600	Weak transcription	HepG2	liver
8	chr15:39888400-39891800	Weak transcription	Pancreas	Pancrea
9	chr15:39888400-39892000	Weak transcription	Fetal Lung	lung
10	chr15:39888400-39899200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:39888400-39899200	Weak transcription	Esophagus	oesophagus
12	chr15:39888400-39899200	Weak transcription	Left Ventricle	heart
13	chr15:39888400-39900600	Weak transcription	Fetal Brain Female	brain
14	chr15:39888400-39901000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:39888400-39901000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:39888600-39892200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:39888800-39891600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:39888800-39891600	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:39888800-39891600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:39888800-39892200	Weak transcription	HSMMtube	muscle
21	chr15:39888800-39894400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:39889000-39891400	Weak transcription	HUVEC	blood vessel
23	chr15:39889000-39891800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:39889000-39891800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:39889200-39891800	Weak transcription	Osteobl	bone
26	chr15:39889200-39901200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:39889400-39891800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:39889600-39891800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:39889800-39892000	Enhancers	Fetal Intestine Large	intestine
30	chr15:39889800-39893200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:39890200-39891800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:39890200-39891800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:39890200-39891800	Weak transcription	NHLF	lung
34	chr15:39890200-39892000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:39890200-39892000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:39890200-39892000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:39890200-39892000	Weak transcription	NH-A	brain
38	chr15:39890200-39900800	Weak transcription	HMEC	breast
39	chr15:39890400-39891400	Weak transcription	A549	lung
40	chr15:39890400-39892000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:39890400-39892000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:39890400-39892200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:39890400-39892200	Weak transcription	HSMM	muscle
44	chr15:39890600-39897000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:39890800-39891600	Weak transcription	Colon Smooth Muscle	Colon
46	chr15:39890800-39892200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr15:39891000-39891800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:39891200-39891400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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