Variant report

Variant	rs55716459
Chromosome Location	chr15:77710907-77710908
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	chr15:77710839-77711062	ProgFib	skin:	n/a	n/a
2	POLR2A	chr15:77710728-77713515	IMR90	lung:	n/a	n/a
3	MAZ	chr15:77710652-77714451	IMR90	lung:	n/a	chr15:77711944-77711954 chr15:77712740-77712750
4	POLR2A	chr15:77710704-77711031	HUVEC	blood vessel:	n/a	n/a
5	RAD21	chr15:77710639-77712623	IMR90	lung:	n/a	chr15:77711533-77711547
6	ARID3A	chr15:77710819-77710914	HepG2	liver:	n/a	n/a
7	CTCF	chr15:77710880-77711030	A549	lung:	n/a	n/a
8	POLR2A	chr15:77710478-77711474	HUVEC	blood vessel:	n/a	n/a
9	MTA3	chr15:77710883-77712065	GM12878	blood:	n/a	n/a
10	FOS	chr15:77710774-77710995	MCF10A-Er-Src	breast:	n/a	n/a
11	MXI1	chr15:77710812-77714549	SK-N-SH	brain:	n/a	n/a
12	HCFC1	chr15:77710661-77714679	Hela-S3	cervix:	n/a	n/a
13	GATA3	chr15:77709823-77711753	SK-N-SH	brain:	n/a	chr15:77710536-77710545 chr15:77710536-77710543 chr15:77710536-77710543 chr15:77710536-77710543
14	POLR2A	chr15:77710654-77711027	HUVEC	blood vessel:	n/a	n/a
15	GATA3	chr15:77709905-77711012	SK-N-SH	brain:	n/a	chr15:77710536-77710545 chr15:77710536-77710543 chr15:77710536-77710543 chr15:77710536-77710543
16	MXI1	chr15:77710378-77714696	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:77709022..77711510-chr15:77717279..77719349,2	K562	blood:
2	chr15:77695120..77697268-chr15:77709701..77711591,2	K562	blood:
3	chr15:77701664..77703699-chr15:77708996..77711356,2	MCF-7	breast:
4	chr15:77688577..77690434-chr15:77709040..77711857,2	K562	blood:

Variant related genes	Relation type
HMG20A	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10519164	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519167	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11629652	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11629835	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11630843	0.82[ASN][1000 genomes]
rs11631909	0.82[ASN][1000 genomes]
rs11632729	0.84[AMR][1000 genomes]
rs11634056	0.82[ASN][1000 genomes]
rs11636412	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11639308	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12898281	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12899552	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12903253	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1554051	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16968835	0.84[AMR][1000 genomes]
rs17383727	0.82[ASN][1000 genomes]
rs17383984	0.82[ASN][1000 genomes]
rs17384406	0.82[ASN][1000 genomes]
rs17385550	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17385648	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17469276	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17470228	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2864082	0.82[ASN][1000 genomes]
rs34194537	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34981488	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35235292	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35268067	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35490414	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35902242	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62007263	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62008432	0.82[ASN][1000 genomes]
rs71407208	0.97[ASN][1000 genomes]
rs7162362	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7176254	0.82[ASN][1000 genomes]
rs8032071	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' 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
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv21291	chr15:77707945-77712363	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55716459	RP11-797A18.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77698600-77711200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:77702600-77711000	Weak transcription	Lung	lung
3	chr15:77702800-77711000	Weak transcription	Aorta	Aorta
4	chr15:77703000-77711400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:77707800-77711000	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr15:77708200-77711400	Weak transcription	Gastric	stomach
7	chr15:77708200-77711400	Weak transcription	Pancreas	Pancrea
8	chr15:77708200-77711400	Weak transcription	Spleen	Spleen
9	chr15:77708400-77711200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr15:77708800-77711200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr15:77709000-77711200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:77709400-77711000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:77709400-77711400	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr15:77709400-77711600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:77709600-77711000	Weak transcription	Liver	Liver
16	chr15:77709600-77711200	Flanking Active TSS	HUVEC	blood vessel
17	chr15:77709600-77712600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:77709600-77713800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:77709800-77711000	Flanking Active TSS	Osteobl	bone
20	chr15:77709800-77711400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr15:77710000-77711000	Enhancers	Brain Substantia Nigra	brain
22	chr15:77710000-77711000	Enhancers	Thymus	Thymus
23	chr15:77710000-77711200	Flanking Active TSS	Fetal Lung	lung
24	chr15:77710000-77711200	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr15:77710000-77711200	Flanking Active TSS	NH-A	brain
26	chr15:77710000-77711400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:77710000-77711400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:77710200-77711000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr15:77710200-77711400	Weak transcription	Small Intestine	intestine
30	chr15:77710200-77711600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr15:77710200-77713600	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr15:77710200-77714400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:77710200-77714400	Active TSS	Right Atrium	heart
34	chr15:77710400-77711000	Enhancers	Stomach Mucosa	stomach
35	chr15:77710400-77711000	Flanking Active TSS	K562	blood
36	chr15:77710400-77711200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr15:77710400-77711200	Enhancers	Primary T cells from cord blood	blood
38	chr15:77710400-77711600	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr15:77710400-77713800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:77710400-77714400	Active TSS	Right Ventricle	heart
41	chr15:77710400-77714400	Active TSS	NHDF-Ad	bronchial
42	chr15:77710400-77714600	Active TSS	NHLF	lung
43	chr15:77710600-77711000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:77710600-77711000	Enhancers	Primary hematopoietic stem cells	blood
45	chr15:77710600-77711000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:77710600-77711000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:77710600-77711000	Flanking Active TSS	Fetal Stomach	stomach
48	chr15:77710600-77711200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr15:77710600-77711200	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr15:77710600-77711200	Flanking Active TSS	Fetal Heart	heart

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