Variant report

Variant	rs62120691
Chromosome Location	chr19:39972766-39972767
allele	A/G
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:17)
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	chr19:39972644-39972862	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
3	MYC	chr19:39970732-39973093	A549	lung:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
4	SIN3AK20	chr19:39970475-39973057	PANC-1	pancreas:	n/a	n/a
5	HEY1	chr19:39972574-39972845	K562	blood:	n/a	n/a
6	ESRRA	chr19:39970619-39973183	GM12878	blood:	n/a	chr19:39972390-39972403
7	SIN3AK20	chr19:39970208-39973088	PANC-1	pancreas:	n/a	n/a
8	REST	chr19:39970787-39973063	PANC-1	pancreas:	n/a	chr19:39971694-39971708

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39934091..39937562-chr19:39970121..39972977,5	K562	blood:
2	chr19:39934091..39937114-chr19:39969895..39972879,3	K562	blood:
3	chr19:39969179..39972823-chr19:40019268..40024259,8	K562	blood:
4	chr19:39962317..39966816-chr19:39969995..39972771,6	MCF-7	breast:
5	chr19:39970388..39973416-chr19:39987093..39991960,6	MCF-7	breast:
6	chr19:39881392..39883533-chr19:39972449..39976025,3	K562	blood:
7	chr19:39971121..39973511-chr19:39973741..39976891,3	MCF-7	breast:
8	chr19:39923294..39928217-chr19:39969939..39976745,7	K562	blood:
9	chr19:39934676..39937838-chr19:39970025..39973557,7	MCF-7	breast:
10	chr19:39924549..39928313-chr19:39970394..39973544,4	MCF-7	breast:
11	chr19:39969762..39972823-chr19:40020818..40024781,5	K562	blood:
12	chr19:39971313..39973393-chr19:39989065..39991077,2	MCF-7	breast:
13	chr19:39956900..39963294-chr19:39968062..39973681,7	MCF-7	breast:
14	chr19:39965047..39968880-chr19:39971509..39974367,5	MCF-7	breast:
15	chr19:39934619..39937838-chr19:39970480..39972998,6	MCF-7	breast:
16	chr19:39960496..39962184-chr19:39970692..39973089,3	MCF-7	breast:
17	chr19:39925979..39927964-chr19:39971323..39973932,2	K562	blood:

No data

Variant related genes	Relation type
TIMM50	TF binding region
ENSG00000269792	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000176401	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10420073	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10423161	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10423921	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10425652	0.82[ASN][1000 genomes]
rs10426543	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11882744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529733	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3786950	0.82[ASN][1000 genomes]
rs45568533	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802030	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802033	0.84[ASN][1000 genomes]
rs4803244	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803248	0.84[ASN][1000 genomes]
rs59269050	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61480418	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7245986	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7246329	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73035459	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73035461	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8106642	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 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	chr19:39971000-39973000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:39971200-39973000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr19:39971400-39973000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:39971600-39972800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:39971600-39972800	Flanking Active TSS	Colonic Mucosa	Colon
6	chr19:39971600-39973000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
7	chr19:39971800-39972800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:39971800-39972800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr19:39971800-39972800	Flanking Active TSS	Liver	Liver
10	chr19:39971800-39972800	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr19:39971800-39972800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr19:39971800-39972800	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr19:39972000-39972800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:39972000-39972800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr19:39972000-39972800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr19:39972000-39972800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr19:39972000-39972800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:39972000-39972800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr19:39972000-39972800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:39972000-39972800	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr19:39972000-39972800	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr19:39972000-39972800	Flanking Active TSS	Brain Germinal Matrix	brain
23	chr19:39972000-39972800	Flanking Active TSS	Brain Substantia Nigra	brain
24	chr19:39972000-39972800	Flanking Active TSS	Fetal Lung	lung
25	chr19:39972000-39972800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr19:39972000-39972800	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr19:39972000-39972800	Flanking Active TSS	Stomach Mucosa	stomach
28	chr19:39972000-39972800	Flanking Active TSS	HUVEC	blood vessel
29	chr19:39972000-39972800	Flanking Active TSS	K562	blood
30	chr19:39972000-39972800	Flanking Active TSS	Osteobl	bone
31	chr19:39972000-39973000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:39972000-39973000	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr19:39972000-39973000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr19:39972000-39973000	Flanking Active TSS	Dnd41	blood
35	chr19:39972200-39972800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
36	chr19:39972200-39972800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:39972200-39972800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr19:39972200-39972800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:39972200-39972800	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr19:39972200-39972800	Flanking Active TSS	GM12878-XiMat	blood
41	chr19:39972200-39972800	Flanking Active TSS	HMEC	breast
42	chr19:39972200-39972800	Flanking Active TSS	NHLF	lung
43	chr19:39972200-39973000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:39972200-39973000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:39972200-39973000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:39972200-39973000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:39972200-39973000	Flanking Active TSS	Hela-S3	cervix
48	chr19:39972200-39986400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr19:39972400-39972800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:39972400-39972800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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