Variant report

Variant	rs74025200
Chromosome Location	chr15:77710768-77710769
allele	A/C
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	chr15:77710728-77713515	IMR90	lung:	n/a	n/a
2	MAZ	chr15:77710652-77714451	IMR90	lung:	n/a	chr15:77711944-77711954 chr15:77712740-77712750
3	POLR2A	chr15:77710704-77711031	HUVEC	blood vessel:	n/a	n/a
4	RAD21	chr15:77710639-77712623	IMR90	lung:	n/a	chr15:77711533-77711547
5	TCF7L2	chr15:77710381-77710873	HEK293	kidney:	n/a	chr15:77710521-77710537 chr15:77710522-77710536
6	POLR2A	chr15:77710478-77711474	HUVEC	blood vessel:	n/a	n/a
7	HCFC1	chr15:77710661-77714679	Hela-S3	cervix:	n/a	n/a
8	GATA3	chr15:77709823-77711753	SK-N-SH	brain:	n/a	chr15:77710536-77710545 chr15:77710536-77710543 chr15:77710536-77710543 chr15:77710536-77710543
9	POLR2A	chr15:77710654-77711027	HUVEC	blood vessel:	n/a	n/a
10	GATA3	chr15:77709905-77711012	SK-N-SH	brain:	n/a	chr15:77710536-77710545 chr15:77710536-77710543 chr15:77710536-77710543 chr15:77710536-77710543
11	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: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10162742	1.00[AMR][1000 genomes]
rs12324632	0.83[AFR][1000 genomes]
rs28542588	1.00[AMR][1000 genomes]
rs74025198	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74025199	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74026921	1.00[AFR][1000 genomes];1.00[AMR][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

No data

Chromatin state (count:106 , 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	chr15:77703200-77710800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:77704800-77710800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:77707200-77710800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr15:77707800-77710800	Enhancers	Brain Hippocampus Middle	brain
9	chr15:77707800-77711000	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr15:77708000-77710800	Weak transcription	Placenta	Placenta
11	chr15:77708200-77710800	Enhancers	HSMM	muscle
12	chr15:77708200-77711400	Weak transcription	Gastric	stomach
13	chr15:77708200-77711400	Weak transcription	Pancreas	Pancrea
14	chr15:77708200-77711400	Weak transcription	Spleen	Spleen
15	chr15:77708400-77710800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr15:77708400-77711200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr15:77708800-77710800	Weak transcription	Primary B cells from cord blood	blood
18	chr15:77708800-77711200	Enhancers	H9 Cell Line	embryonic stem cell
19	chr15:77709000-77710800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr15:77709000-77710800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:77709000-77710800	Enhancers	NHEK	skin
22	chr15:77709000-77711200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:77709200-77710800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:77709200-77710800	Enhancers	HMEC	breast
25	chr15:77709400-77710800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:77709400-77710800	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr15:77709400-77710800	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr15:77709400-77710800	Enhancers	Hela-S3	cervix
29	chr15:77709400-77711000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr15:77709400-77711400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr15:77709400-77711600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:77709600-77711000	Weak transcription	Liver	Liver
33	chr15:77709600-77711200	Flanking Active TSS	HUVEC	blood vessel
34	chr15:77709600-77712600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:77709600-77713800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:77709800-77710800	Enhancers	HepG2	liver
37	chr15:77709800-77711000	Flanking Active TSS	Osteobl	bone
38	chr15:77709800-77711400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr15:77710000-77710800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr15:77710000-77710800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:77710000-77710800	Weak transcription	Left Ventricle	heart
42	chr15:77710000-77710800	Enhancers	Rectal Smooth Muscle	rectum
43	chr15:77710000-77710800	Enhancers	Stomach Smooth Muscle	stomach
44	chr15:77710000-77711000	Enhancers	Brain Substantia Nigra	brain
45	chr15:77710000-77711000	Enhancers	Thymus	Thymus
46	chr15:77710000-77711200	Flanking Active TSS	Fetal Lung	lung
47	chr15:77710000-77711200	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr15:77710000-77711200	Flanking Active TSS	NH-A	brain
49	chr15:77710000-77711400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:77710000-77711400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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