Variant report

Variant	rs1051442
Chromosome Location	chr15:39887649-39887650
allele	C/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	chr15:39887532-39889262	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:39887572-39888998	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr15:39887555-39887675	SK-N-SH	brain:	n/a	n/a
5	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
6	POLR2A	chr15:39872827-39889306	SK-N-SH	brain:	n/a	n/a
7	STAT3	chr15:39887530-39887693	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr15:39887473-39888568	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr15:39871636-39892218	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:39871327-39893495	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr15:39887322-39891967	MCF-7	breast:	n/a	n/a
12	POLR2A	chr15:39870574-39892778	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr15:39871778-39892493	ProgFib	skin:	n/a	n/a
14	POLR2A	chr15:39871484-39892179	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr15:39871294-39893132	IMR90	lung:	n/a	n/a
16	CTCF	chr15:39887580-39887730	HRPEpiC	eye:	n/a	n/a
17	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39885481..39888433-chr15:39892783..39894545,2	K562	blood:
2	chr15:39886322..39888433-chr15:39891587..39894545,2	K562	blood:

Variant related genes	Relation type
ENSG00000259279	TF binding region
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10152903	1.00[CHB][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs10152951	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1038097	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10520143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10520146	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs10520147	1.00[CHB][hapmap]
rs10520148	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs1073675	1.00[CHB][hapmap]
rs12438058	1.00[ASN][1000 genomes]
rs12442155	1.00[ASN][1000 genomes]
rs12442221	1.00[ASN][1000 genomes]
rs1382443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382444	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969143	1.00[ASN][1000 genomes]
rs16969167	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16969487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16969491	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16969547	1.00[CHB][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs16969663	1.00[CHB][hapmap]
rs16969664	1.00[CHB][hapmap]
rs16969666	1.00[CHB][hapmap]
rs16969672	1.00[CHB][hapmap]
rs16969679	1.00[CHB][hapmap]
rs16969680	1.00[CHB][hapmap]
rs16969688	1.00[CHB][hapmap]
rs17631807	1.00[ASN][1000 genomes]
rs17632916	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17633107	1.00[CEU][hapmap];1.00[CHB][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]
rs17633210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17702987	1.00[ASN][1000 genomes]
rs17705806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17706083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17706179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1813493	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988082	0.83[EUR][1000 genomes]
rs1988555	0.86[EUR][1000 genomes]
rs1994380	1.00[CHB][hapmap]
rs2129457	1.00[CHB][hapmap]
rs2228262	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs2228263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2618156	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618160	0.93[EUR][1000 genomes]
rs2618161	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618164	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs2618165	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2618166	1.00[ASN][1000 genomes]
rs2618167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664123	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664136	0.92[EUR][1000 genomes]
rs2664137	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664138	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs2664140	0.93[EUR][1000 genomes]
rs2664142	0.93[EUR][1000 genomes]
rs28377784	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28549326	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28619289	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28622135	1.00[ASN][1000 genomes]
rs28653011	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34878675	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35275624	1.00[ASN][1000 genomes]
rs41315060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319740	0.83[CEU][hapmap]
rs4415979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4503768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs45461294	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4923835	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58188999	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59578395	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59628570	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62002368	1.00[ASN][1000 genomes]
rs62002377	1.00[ASN][1000 genomes]
rs62002378	1.00[ASN][1000 genomes]
rs62002379	1.00[ASN][1000 genomes]
rs62002380	1.00[ASN][1000 genomes]
rs62002384	1.00[ASN][1000 genomes]
rs6492905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7172155	1.00[CHB][hapmap]
rs7173948	1.00[CHB][hapmap]
rs7179604	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7181354	1.00[CHB][hapmap]
rs7182423	1.00[CHB][hapmap]
rs74008526	1.00[ASN][1000 genomes]
rs74008647	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74008648	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8041266	1.00[CHB][hapmap]
rs880270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs937961	1.00[CHB][hapmap]
rs937962	1.00[CHB][hapmap]
rs954152	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9972350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.93[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:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39874800-39889200	Weak transcription	Brain Substantia Nigra	brain
2	chr15:39875000-39889400	Weak transcription	Brain Anterior Caudate	brain
3	chr15:39875200-39887800	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr15:39875200-39888400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:39875200-39889800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:39875600-39889000	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr15:39875600-39890200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:39875600-39890400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:39875800-39889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:39876000-39888600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:39876200-39888200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:39876200-39890200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:39876200-39890400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:39877200-39890400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:39877800-39888200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:39877800-39888600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:39878000-39888400	Strong transcription	Left Ventricle	heart
18	chr15:39878000-39890200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:39878200-39888400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:39878400-39888400	Strong transcription	NHEK	skin
21	chr15:39878600-39888400	Strong transcription	HepG2	liver
22	chr15:39878600-39888800	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr15:39879000-39888800	Strong transcription	Fetal Muscle Leg	muscle
24	chr15:39879200-39888400	Strong transcription	Adipose Nuclei	Adipose
25	chr15:39879200-39888400	Strong transcription	Fetal Lung	lung
26	chr15:39879800-39889400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:39880000-39888000	Strong transcription	Fetal Heart	heart
28	chr15:39880200-39889400	ZNF genes & repeats	Fetal Intestine Large	intestine
29	chr15:39880600-39887800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:39880600-39887800	Strong transcription	Ovary	ovary
31	chr15:39880800-39888600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr15:39880800-39890200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:39881000-39888800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:39881400-39888400	Strong transcription	Right Ventricle	heart
35	chr15:39881400-39888800	Strong transcription	Liver	Liver
36	chr15:39881400-39889200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr15:39882000-39889800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:39882200-39888200	Strong transcription	Esophagus	oesophagus
39	chr15:39882200-39888400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr15:39882200-39889800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:39883000-39889000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:39883400-39888400	Strong transcription	Fetal Brain Female	brain
43	chr15:39883600-39888200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr15:39883600-39888400	Strong transcription	Rectal Smooth Muscle	rectum
45	chr15:39883800-39888200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:39884000-39888000	Weak transcription	Thymus	Thymus
47	chr15:39884200-39888200	Weak transcription	Brain Hippocampus Middle	brain
48	chr15:39884400-39889400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr15:39884800-39890600	Genic enhancers	Rectal Mucosa Donor 31	rectum
50	chr15:39885200-39891000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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