Variant report

Variant	rs10420252
Chromosome Location	chr19:36139172-36139173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:390)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:390 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr19:36138785-36139548	K562	blood:	n/a	n/a
2	MAZ	chr19:36138807-36139440	K562	blood:	n/a	n/a
3	POLR2A	chr19:36139075-36139400	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:36138821-36139453	K562	blood:	n/a	n/a
5	IRF3	chr19:36139012-36139264	HepG2	liver:	n/a	chr19:36139123-36139137
6	JUN	chr19:36138647-36140356	K562	blood:	n/a	n/a
7	MAX	chr19:36138859-36139471	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr19:36138800-36139436	HCT-116	colon:	n/a	n/a
9	TAF1	chr19:36138843-36139854	K562	blood:	n/a	n/a
10	GABPA	chr19:36138945-36139443	HepG2	liver:	n/a	chr19:36139230-36139237
11	PAX5	chr19:36138974-36139335	GM12878	blood:	n/a	n/a
12	MAZ	chr19:36138858-36139375	Hela-S3	cervix:	n/a	n/a
13	ZMIZ1	chr19:36138840-36139596	K562	blood:	n/a	n/a
14	NRF1	chr19:36138880-36139233	K562	blood:	n/a	chr19:36139049-36139060
15	CBX3	chr19:36138876-36139440	K562	blood:	n/a	n/a
16	FOSL2	chr19:36138757-36139650	A549	lung:	n/a	n/a
17	POLR2A	chr19:36138709-36139509	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr19:36138868-36140069	K562	blood:	n/a	n/a
19	SP1	chr19:36138679-36139552	A549	lung:	n/a	chr19:36139124-36139134
20	FOS	chr19:36138890-36139296	K562	blood:	n/a	n/a
21	MYC	chr19:36138892-36139346	MCF10A-Er-Src	breast:	n/a	n/a
22	STAT5A	chr19:36139022-36139767	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:36138744-36139970	K562	blood:	n/a	n/a
24	FOXM1	chr19:36139062-36139484	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:36138795-36139484	GM19099	blood:	n/a	n/a
26	SIN3A	chr19:36139048-36139983	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr19:36138912-36139501	SK-N-SH	brain:	n/a	n/a
28	BCL3	chr19:36138839-36139698	A549	lung:	n/a	n/a
29	TAF1	chr19:36138816-36139427	GM12878	blood:	n/a	n/a
30	PBX3	chr19:36138924-36139259	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:36138854-36139525	GM12891	blood:	n/a	n/a
32	MAX	chr19:36138806-36139691	A549	lung:	n/a	n/a
33	NR2F2	chr19:36138648-36139898	K562	blood:	n/a	n/a
34	TCF7L2	chr19:36139095-36139683	PANC-1	pancreas:	n/a	n/a
35	TAF1	chr19:36138908-36139480	Hela-S3	cervix:	n/a	n/a
36	THAP1	chr19:36139015-36139282	K562	blood:	n/a	n/a
37	GTF2F1	chr19:36138977-36139811	K562	blood:	n/a	n/a
38	POLR2A	chr19:36138836-36139611	GM12892	blood:	n/a	n/a
39	SMC3	chr19:36138970-36139395	Hela-S3	cervix:	n/a	n/a
40	PBX3	chr19:36138930-36139205	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:36138814-36139481	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:36139122-36139319	H1-hESC	embryonic stem cell:	n/a	n/a
43	REST	chr19:36139074-36139434	K562	blood:	n/a	n/a
44	JUND	chr19:36138815-36139445	K562	blood:	n/a	n/a
45	FOS	chr19:36138944-36139363	MCF10A-Er-Src	breast:	n/a	n/a
46	PML	chr19:36138881-36139410	GM12878	blood:	n/a	n/a
47	MYC	chr19:36139084-36139336	HepG2	liver:	n/a	n/a
48	TAF1	chr19:36139098-36139376	SK-N-SH	brain:	n/a	n/a
49	MAX	chr19:36138728-36140358	A549	lung:	n/a	n/a
50	ETS1	chr19:36139105-36139361	K562	blood:	n/a	chr19:36139165-36139178 chr19:36139230-36139241 chr19:36139210-36139223 chr19:36139231-36139242 chr19:36139213-36139222

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36136475..36140054-chr19:36207952..36210367,3	MCF-7	breast:
2	chr19:36138960..36141162-chr19:36141370..36144327,2	K562	blood:
3	chr19:36138864..36139506-chr5:10249390..10250015,2	Hela-S3	cervix:
4	chr19:36118346..36121729-chr19:36137061..36140850,4	MCF-7	breast:
5	chr19:36139069..36141047-chr19:36162643..36164657,2	MCF-7	breast:
6	chr11:82868167..82868671-chr19:36139063..36139883,2	Hela-S3	cervix:
7	chr17:16118306..16119162-chr19:36139052..36139638,2	Hela-S3	cervix:
8	chr19:36138557..36139693-chr20:30192263..30193304,3	Hela-S3	cervix:
9	chr19:36139097..36139639-chr21:34775453..34776328,2	Hela-S3	cervix:
10	chr16:87425396..87426204-chr19:36138957..36139947,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
COX6B1	TF binding region
ENSG00000272333	Chromatin interaction
ENSG00000226510	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000150756	Chromatin interaction
ENSG00000165494	Chromatin interaction
ENSG00000141027	Chromatin interaction
ENSG00000126267	Chromatin interaction
ENSG00000159128	Chromatin interaction
ENSG00000126254	Chromatin interaction
ENSG00000103264	Chromatin interaction
ENSG00000140941	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10403109	0.82[EUR][1000 genomes]
rs10415370	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10418323	0.83[EUR][1000 genomes]
rs10418680	0.83[EUR][1000 genomes]
rs10420286	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs12459935	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs1544332	1.00[CEU][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2267585	0.91[JPT][hapmap]
rs2285419	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2311873	0.85[CEU][hapmap]
rs6510502	1.00[CEU][hapmap]
rs7249516	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36136000-36139200	Weak transcription	Small Intestine	intestine
2	chr19:36136400-36139200	Weak transcription	Fetal Heart	heart
3	chr19:36136400-36139200	Weak transcription	NHDF-Ad	bronchial
4	chr19:36136600-36139200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:36136600-36139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:36136600-36139200	Weak transcription	Gastric	stomach
7	chr19:36136600-36139200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr19:36136600-36139200	Weak transcription	Spleen	Spleen
9	chr19:36138400-36139200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:36138400-36139200	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr19:36138400-36139400	Active TSS	Fetal Brain Female	brain
12	chr19:36138400-36139600	Active TSS	Stomach Smooth Muscle	stomach
13	chr19:36138400-36139800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:36138400-36139800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:36138400-36140400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr19:36138400-36140400	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr19:36138600-36139200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr19:36138600-36139200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:36138600-36139200	Enhancers	Stomach Mucosa	stomach
20	chr19:36138600-36139200	Active TSS	HepG2	liver
21	chr19:36138600-36139800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:36138600-36139800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:36138600-36139800	Active TSS	Brain Anterior Caudate	brain
24	chr19:36138600-36139800	Active TSS	Brain Hippocampus Middle	brain
25	chr19:36138600-36139800	Active TSS	Fetal Lung	lung
26	chr19:36138600-36139800	Active TSS	Rectal Smooth Muscle	rectum
27	chr19:36138600-36140000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr19:36138600-36140000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:36138600-36140000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:36138600-36140000	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr19:36138600-36140000	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr19:36138600-36140000	Active TSS	Aorta	Aorta
33	chr19:36138600-36140000	Active TSS	Fetal Kidney	kidney
34	chr19:36138600-36140000	Active TSS	K562	blood
35	chr19:36138600-36140200	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr19:36138600-36140200	Active TSS	H1 Cell Line	embryonic stem cell
37	chr19:36138600-36140200	Active TSS	H9 Cell Line	embryonic stem cell
38	chr19:36138600-36140200	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr19:36138600-36140200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:36138600-36140200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:36138600-36140200	Active TSS	Colonic Mucosa	Colon
42	chr19:36138600-36140200	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr19:36138600-36140200	Active TSS	Psoas Muscle	Psoas
44	chr19:36138600-36140400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr19:36138600-36140400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:36138600-36140400	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr19:36138600-36140400	Active TSS	A549	lung
48	chr19:36138600-36140600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:36138600-36140600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:36138800-36139200	Flanking Active TSS	Primary B cells from peripheral blood	blood

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