Variant report

Variant	rs12980086
Chromosome Location	chr19:39442992-39442993
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39442638-39443902	HepG2	liver:	n/a	n/a
2	FOSL2	chr19:39442804-39443743	HepG2	liver:	n/a	n/a
3	BCL3	chr19:39442739-39443877	A549	lung:	n/a	n/a
4	CTCF	chr19:39442960-39443110	HCPEpiC	choroid plexus:	n/a	n/a
5	JUN	chr19:39442957-39443144	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:39442686-39444049	HepG2	liver:	n/a	n/a
7	CTCF	chr19:39442960-39443110	HEEpiC	esophagus:	n/a	n/a
8	POLR2A	chr19:39442317-39445459	HepG2	liver:	n/a	n/a
9	CTCF	chr19:39442860-39443010	A549	lung:	n/a	n/a
10	MBD4	chr19:39442776-39443418	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:39428415-39444124	PANC-1	pancreas:	n/a	n/a
12	CTCF	chr19:39442920-39443070	GM12873	blood:	n/a	n/a
13	CTCF	chr19:39442900-39443050	GM12874	blood:	n/a	n/a
14	RAD21	chr19:39442909-39443774	A549	lung:	n/a	n/a
15	CTCF	chr19:39442730-39443979	A549	lung:	n/a	n/a
16	POLR2A	chr19:39442761-39443265	HepG2	liver:	n/a	n/a
17	HEY1	chr19:39442956-39443609	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39420306..39422739-chr19:39440304..39443002,2	K562	blood:

No data

Variant related genes	Relation type
FBXO17	TF binding region
ENSG00000269547	TF binding region
SARS2	TF binding region
ENSG00000128626	Chromatin interaction
ENSG00000104835	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10424843	0.91[EUR][1000 genomes]
rs12052182	0.85[AMR][1000 genomes]
rs12151188	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12982957	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12985638	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7245863	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7249668	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7254599	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
2	chr19:39435800-39453000	Weak transcription	K562	blood
3	chr19:39437200-39443000	Weak transcription	HSMM	muscle
4	chr19:39438200-39447000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:39438400-39453000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:39439200-39452600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:39439600-39446200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:39441000-39443400	Weak transcription	HMEC	breast
9	chr19:39441000-39444400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:39441000-39453000	Weak transcription	Aorta	Aorta
11	chr19:39441000-39459200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:39441200-39443200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:39441200-39443400	Weak transcription	NH-A	brain
14	chr19:39441200-39446400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:39441200-39447600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:39441200-39448200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:39441200-39449200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:39441200-39449200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr19:39441200-39450400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:39441200-39452800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr19:39441200-39453000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:39441200-39453000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:39441200-39453000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:39441200-39453000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:39441200-39453000	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:39441200-39453000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:39441200-39453000	Weak transcription	Lung	lung
28	chr19:39441200-39453000	Weak transcription	Pancreas	Pancrea
29	chr19:39441200-39453000	Weak transcription	Osteobl	bone
30	chr19:39441200-39455800	Weak transcription	Psoas Muscle	Psoas
31	chr19:39441200-39459400	Weak transcription	Fetal Lung	lung
32	chr19:39441200-39465200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr19:39441200-39465200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr19:39441200-39465200	Weak transcription	NHLF	lung
35	chr19:39441200-39465400	Weak transcription	Right Atrium	heart
36	chr19:39441400-39443000	Strong transcription	Fetal Intestine Small	intestine
37	chr19:39441400-39444200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:39441400-39445800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:39441400-39447600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:39441400-39447600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr19:39441400-39452600	Weak transcription	Adipose Nuclei	Adipose
42	chr19:39441400-39452600	Weak transcription	Colon Smooth Muscle	Colon
43	chr19:39441400-39453000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:39441400-39453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr19:39441400-39453000	Weak transcription	Fetal Brain Male	brain
46	chr19:39441400-39453000	Weak transcription	Fetal Brain Female	brain
47	chr19:39441400-39453000	Weak transcription	Ovary	ovary
48	chr19:39441400-39453000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr19:39441400-39453200	Weak transcription	Fetal Heart	heart
50	chr19:39441400-39462000	Weak transcription	Small Intestine	intestine

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