Variant report

Variant	rs60731897
Chromosome Location	chr19:38269259-38269260
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38269182-38270883	HepG2	liver:	n/a	n/a
2	HCFC1	chr19:38269236-38271180	Hela-S3	cervix:	n/a	n/a
3	MAX	chr19:38269235-38270817	HepG2	liver:	n/a	n/a
4	MYC	chr19:38269256-38269591	MCF10A-Er-Src	breast:	n/a	n/a
5	MAX	chr19:38269226-38270930	A549	lung:	n/a	n/a
6	SIX5	chr19:38269120-38270827	A549	lung:	n/a	n/a
7	MXI1	chr19:38269054-38271214	SK-N-SH	brain:	n/a	n/a
8	MXI1	chr19:38269191-38270922	IMR90	lung:	n/a	n/a

No data

(count:5 , 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	chr19:37956743..37958791-chr19:38268721..38270290,2	K562	blood:
4	chr19:38259097..38263090-chr19:38267286..38270188,4	K562	blood:
5	chr19:37995858..37997705-chr19:38268751..38270937,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF573	TF binding region
ENSG00000267422	TF binding region
ENSG00000196437	Chromatin interaction
ENSG00000171827	Chromatin interaction
ENSG00000266916	Chromatin interaction
ENSG00000171817	Chromatin interaction
ENSG00000180479	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1056405	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11083430	0.81[ASN][1000 genomes]
rs11083434	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11665869	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11666021	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11666662	0.81[ASN][1000 genomes]
rs11672440	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12459013	0.81[ASN][1000 genomes]
rs12460735	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1478462	0.81[ASN][1000 genomes]
rs17249047	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs241935	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs241952	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs241954	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs241955	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35205379	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3848624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4088299	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4356596	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4510143	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254809	0.92[EUR][1000 genomes]
rs73025630	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73027418	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73035158	0.81[ASN][1000 genomes]
rs73037036	0.81[ASN][1000 genomes]
rs73039018	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73041004	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs73041022	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73041034	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73041045	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73041047	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8103383	0.93[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	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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
2	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
3	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
4	chr19:38248800-38269400	Weak transcription	NH-A	brain
5	chr19:38249800-38269400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:38251800-38269400	Weak transcription	Gastric	stomach
7	chr19:38251800-38269400	Weak transcription	HUVEC	blood vessel
8	chr19:38252200-38269400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:38254600-38269400	Weak transcription	Right Ventricle	heart
10	chr19:38256800-38269400	Weak transcription	NHLF	lung
11	chr19:38259200-38269400	Weak transcription	Psoas Muscle	Psoas
12	chr19:38260800-38269400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:38260800-38269400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr19:38261200-38269400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:38261200-38269400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:38261200-38269400	Weak transcription	Esophagus	oesophagus
17	chr19:38261200-38269400	Weak transcription	Fetal Muscle Leg	muscle
18	chr19:38261200-38269400	Weak transcription	Placenta	Placenta
19	chr19:38261200-38269400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:38262600-38269400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:38262600-38269400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:38262600-38269400	Weak transcription	Left Ventricle	heart
23	chr19:38263800-38269400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:38264800-38269400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:38265200-38269600	Weak transcription	Ovary	ovary
26	chr19:38265400-38269400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:38268800-38269600	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr19:38269000-38269400	Enhancers	Primary B cells from peripheral blood	blood
29	chr19:38269000-38269400	Enhancers	Primary T cells fromperipheralblood	blood
30	chr19:38269000-38269400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:38269000-38269400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr19:38269000-38269400	Enhancers	Fetal Muscle Trunk	muscle
33	chr19:38269000-38269400	Enhancers	Lung	lung
34	chr19:38269000-38269400	Enhancers	Pancreas	Pancrea
35	chr19:38269000-38269600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr19:38269000-38269600	Enhancers	Spleen	Spleen
37	chr19:38269000-38270000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:38269000-38270000	Flanking Active TSS	Dnd41	blood
39	chr19:38269000-38270800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:38269200-38269400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:38269200-38269400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr19:38269200-38269400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:38269200-38269400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:38269200-38269400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr19:38269200-38269400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr19:38269200-38269400	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr19:38269200-38269400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:38269200-38269400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:38269200-38269400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:38269200-38269400	Enhancers	Brain Substantia Nigra	brain

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