Variant report

Variant	rs62110186
Chromosome Location	chr19:38269873-38269874
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:223)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:223 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr19:38269528-38270531	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:38269619-38270633	Hela-S3	cervix:	n/a	n/a
3	YY1	chr19:38269851-38270521	HCT-116	colon:	n/a	n/a
4	ATF1	chr19:38269848-38270362	K562	blood:	n/a	n/a
5	SIN3AK20	chr19:38269443-38270769	MCF-7	breast:	n/a	n/a
6	E2F6	chr19:38269664-38270877	A549	lung:	n/a	n/a
7	MAX	chr19:38269755-38270637	H1-hESC	embryonic stem cell:	n/a	n/a
8	USF1	chr19:38269841-38270031	SK-N-SH_RA	brain:	n/a	chr19:38269965-38269978
9	POLR2A	chr19:38269704-38270676	GM12878	blood:	n/a	n/a
10	TAF1	chr19:38269699-38270660	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr19:38269754-38270689	K562	blood:	n/a	n/a
12	RCOR1	chr19:38269684-38270392	GM12878	blood:	n/a	n/a
13	MAX	chr19:38269715-38270685	GM12878	blood:	n/a	n/a
14	REST	chr19:38269429-38270828	H1-neurons	neurons:	n/a	chr19:38270079-38270089 chr19:38269734-38269744
15	TBP	chr19:38269728-38270512	GM12878	blood:	n/a	n/a
16	STAT5A	chr19:38269857-38270513	GM12878	blood:	n/a	n/a
17	BHLHE40	chr19:38269709-38270586	K562	blood:	n/a	chr19:38269965-38269978
18	POLR2A	chr19:38269182-38270883	HepG2	liver:	n/a	n/a
19	PAX5	chr19:38269633-38270399	GM12878	blood:	n/a	n/a
20	ETS1	chr19:38269580-38270796	A549	lung:	n/a	chr19:38270640-38270647 chr19:38270067-38270080
21	MYC	chr19:38269766-38269937	MCF-7	breast:	n/a	n/a
22	CTCF	chr19:38269766-38269897	MCF-7	breast:	n/a	n/a
23	MAX	chr19:38269486-38270754	NB4	blood:	n/a	n/a
24	ELK4	chr19:38269805-38270600	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr19:38269641-38270775	HL-60	blood:	n/a	n/a
26	HCFC1	chr19:38269236-38271180	Hela-S3	cervix:	n/a	n/a
27	SP1	chr19:38269683-38270760	A549	lung:	n/a	chr19:38270611-38270620 chr19:38270610-38270622
28	POLR2A	chr19:38269673-38270698	GM12891	blood:	n/a	n/a
29	POLR2A	chr19:38269696-38270678	GM19193	blood:	n/a	n/a
30	POLR2A	chr19:38269678-38270672	ProgFib	skin:	n/a	n/a
31	MYC	chr19:38269768-38270083	MCF-7	breast:	n/a	n/a
32	POLR2A	chr19:38269539-38270651	GM12891	blood:	n/a	n/a
33	POLR2A	chr19:38269712-38270615	HepG2	liver:	n/a	n/a
34	POLR2A	chr19:38269730-38270777	HUVEC	blood vessel:	n/a	n/a
35	YY1	chr19:38269665-38270650	GM12892	blood:	n/a	n/a
36	TBP	chr19:38269284-38270687	Hela-S3	cervix:	n/a	n/a
37	TBP	chr19:38269699-38270759	K562	blood:	n/a	n/a
38	CREB1	chr19:38269653-38270608	A549	lung:	n/a	n/a
39	STAT5A	chr19:38269633-38270460	GM12878	blood:	n/a	n/a
40	ELK1	chr19:38269766-38270475	GM12878	blood:	n/a	n/a
41	CTCF	chr19:38269755-38269892	MCF-7	breast:	n/a	n/a
42	TBL1XR1	chr19:38269634-38270601	GM12878	blood:	n/a	n/a
43	TCF12	chr19:38269807-38270696	A549	lung:	n/a	n/a
44	IRF3	chr19:38269858-38270491	GM12878	blood:	n/a	chr19:38269912-38269926
45	MAX	chr19:38269235-38270817	HepG2	liver:	n/a	n/a
46	RELA	chr19:38269722-38270665	GM19099	blood:	n/a	n/a
47	YY1	chr19:38269576-38270563	GM12891	blood:	n/a	n/a
48	MTA3	chr19:38269524-38270706	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:38269642-38270614	GM12878	blood:	n/a	n/a
50	TCF12	chr19:38269440-38270844	A549	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38085182..38087082-chr19:38268049..38270346,2	K562	blood:
2	chr19:38261551..38263090-chr19:38267286..38270188,2	K562	blood:
3	chr19:38269810..38270643-chrX:77154544..77155428,2	Hela-S3	cervix:
4	chr19:37956743..37958791-chr19:38268721..38270290,2	K562	blood:
5	chr19:38084603..38087452-chr19:38269351..38271925,3	MCF-7	breast:
6	chr19:38259097..38263090-chr19:38267286..38270188,4	K562	blood:
7	chr19:37995858..37997705-chr19:38268751..38270937,2	MCF-7	breast:
8	chr13:111365926..111366706-chr19:38269408..38269951,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000267422	TF binding region
ENSG00000171817	Chromatin interaction
ENSG00000266916	Chromatin interaction
ENSG00000180479	Chromatin interaction
ENSG00000171827	Chromatin interaction
ENSG00000196437	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000131174	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10153500	0.90[EUR][1000 genomes]
rs10424047	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11878261	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879149	0.85[EUR][1000 genomes]
rs11880056	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880604	0.85[EUR][1000 genomes]
rs11883255	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975881	0.84[EUR][1000 genomes]
rs16975930	0.84[EUR][1000 genomes]
rs34206817	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743484	0.82[EUR][1000 genomes]
rs56075341	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56264690	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56281742	0.93[EUR][1000 genomes]
rs57504517	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57725815	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57867853	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59966837	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60686304	0.93[EUR][1000 genomes]
rs62108260	0.93[EUR][1000 genomes]
rs62108262	0.85[EUR][1000 genomes]
rs62108289	0.93[EUR][1000 genomes]
rs62108290	0.93[EUR][1000 genomes]
rs62108292	0.93[EUR][1000 genomes]
rs62108293	0.93[EUR][1000 genomes]
rs62108297	0.93[EUR][1000 genomes]
rs62108348	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62108350	0.95[ASN][1000 genomes]
rs62108354	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110178	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110183	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110187	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110188	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110190	0.84[EUR][1000 genomes]
rs62110192	0.84[EUR][1000 genomes]
rs62110194	0.84[EUR][1000 genomes]
rs62110195	0.84[EUR][1000 genomes]
rs62110222	0.84[EUR][1000 genomes]
rs62111488	0.93[EUR][1000 genomes]
rs62111490	0.93[EUR][1000 genomes]
rs7245965	0.84[EUR][1000 genomes]
rs7245981	0.93[EUR][1000 genomes]
rs7246147	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247175	0.93[EUR][1000 genomes]
rs7247345	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251502	0.84[EUR][1000 genomes]
rs7258992	0.93[EUR][1000 genomes]
rs7259029	0.93[EUR][1000 genomes]
rs7259717	0.93[EUR][1000 genomes]
rs73932929	0.93[EUR][1000 genomes]
rs73932955	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8100469	0.84[EUR][1000 genomes]
rs8101476	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8101991	0.93[EUR][1000 genomes]
rs8102189	0.93[EUR][1000 genomes]
rs8104124	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104747	0.93[EUR][1000 genomes]
rs8108261	0.93[EUR][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 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	chr19:38269000-38270000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:38269000-38270000	Flanking Active TSS	Dnd41	blood
3	chr19:38269000-38270800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38269200-38270000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:38269200-38270000	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr19:38269200-38270000	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr19:38269200-38270000	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr19:38269200-38270000	Flanking Active TSS	Liver	Liver
9	chr19:38269200-38270000	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr19:38269200-38270000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:38269200-38270000	Flanking Active TSS	Fetal Lung	lung
12	chr19:38269200-38270000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr19:38269200-38270200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr19:38269200-38270600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr19:38269200-38270800	Active TSS	Brain Cingulate Gyrus	brain
16	chr19:38269200-38270800	Active TSS	Fetal Intestine Small	intestine
17	chr19:38269200-38270800	Active TSS	HSMM	muscle
18	chr19:38269200-38271000	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr19:38269200-38271000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:38269200-38271000	Active TSS	Brain Hippocampus Middle	brain
21	chr19:38269200-38271000	Active TSS	A549	lung
22	chr19:38269200-38271200	Active TSS	H1 Cell Line	embryonic stem cell
23	chr19:38269200-38271200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:38269200-38271200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:38269200-38271200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr19:38269200-38271200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr19:38269200-38271200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr19:38269200-38271200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr19:38269200-38271200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:38269200-38271200	Active TSS	GM12878-XiMat	blood
31	chr19:38269200-38271200	Active TSS	HMEC	breast
32	chr19:38269200-38271400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:38269400-38270000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:38269400-38270000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr19:38269400-38270000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:38269400-38270000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:38269400-38270000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr19:38269400-38270000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr19:38269400-38270000	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr19:38269400-38270000	Flanking Active TSS	NH-A	brain
41	chr19:38269400-38270800	Active TSS	H9 Cell Line	embryonic stem cell
42	chr19:38269400-38270800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:38269400-38270800	Active TSS	Placenta Amnion	Placenta Amnion
44	chr19:38269400-38271000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr19:38269400-38271000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:38269400-38271000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:38269400-38271000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:38269400-38271200	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr19:38269400-38271200	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr19:38269400-38271200	Active TSS	NHLF	lung

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