Variant report

Variant	rs12462710
Chromosome Location	chr19:39413383-39413384
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39411965-39413469	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:39410749-39413573	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39412811-39414665	K562	blood:	n/a	n/a
4	YY1	chr19:39413325-39413465	K562	blood:	n/a	n/a
5	CHD2	chr19:39413212-39413471	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39338289..39340175-chr19:39412991..39414800,2	K562	blood:
2	chr19:39334351..39336976-chr19:39412590..39415295,2	K562	blood:
3	chr19:39413074..39415034-chr19:39423613..39425226,2	K562	blood:
4	chr19:39341116..39343070-chr19:39413366..39415101,2	K562	blood:
5	chr19:39411214..39414705-chr19:39419221..39421908,4	MCF-7	breast:
6	chr19:39411897..39413585-chr19:39419804..39422534,2	K562	blood:

No data

Variant related genes	Relation type
SARS2	TF binding region
ENSG00000128626	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000269688	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10416055	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425217	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10775533	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083488	0.87[EUR][1000 genomes]
rs11083489	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668245	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609975	0.81[EUR][1000 genomes]
rs12610409	0.92[ASN][1000 genomes]
rs12972986	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979755	0.92[ASN][1000 genomes]
rs12982957	0.80[EUR][1000 genomes]
rs12985428	0.86[EUR][1000 genomes]
rs17545254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808661	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1808662	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865047	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1865049	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3136640	0.92[ASN][1000 genomes]
rs4801971	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802998	0.92[ASN][1000 genomes]
rs4803006	0.92[ASN][1000 genomes]
rs4803034	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257007	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730078	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7508411	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7508539	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113389	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9636109	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9749516	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	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
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv3378202	chr19:39409312-39413510	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12462710	CTC-360G5.9	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
2	chr19:39391600-39414800	Weak transcription	HMEC	breast
3	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
4	chr19:39392400-39414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:39392600-39414600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:39392600-39418800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:39395600-39414800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:39395600-39415000	Weak transcription	Hela-S3	cervix
9	chr19:39398000-39420600	Weak transcription	Psoas Muscle	Psoas
10	chr19:39398600-39415000	Weak transcription	Brain Substantia Nigra	brain
11	chr19:39398800-39415000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr19:39399800-39414800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr19:39399800-39414800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:39400000-39414200	Weak transcription	Left Ventricle	heart
15	chr19:39402800-39420200	Weak transcription	Colon Smooth Muscle	Colon
16	chr19:39403000-39415000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:39403600-39420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:39403800-39420200	Weak transcription	Fetal Brain Male	brain
19	chr19:39405400-39413600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:39406000-39414800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:39406400-39420000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:39406800-39420200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:39409000-39414200	Weak transcription	Colonic Mucosa	Colon
24	chr19:39409000-39417400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:39409200-39419000	Strong transcription	Fetal Intestine Small	intestine
26	chr19:39409200-39420400	Weak transcription	Stomach Mucosa	stomach
27	chr19:39409600-39418400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr19:39410000-39413400	Strong transcription	Primary T cells from cord blood	blood
29	chr19:39410000-39417400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:39410200-39417600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:39410400-39414600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr19:39410600-39414800	Weak transcription	NHDF-Ad	bronchial
33	chr19:39411200-39415000	Weak transcription	HSMM	muscle
34	chr19:39411400-39413400	Strong transcription	Brain Cingulate Gyrus	brain
35	chr19:39411400-39413400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr19:39411400-39415000	Weak transcription	HUVEC	blood vessel
37	chr19:39411400-39419000	Strong transcription	Fetal Stomach	stomach
38	chr19:39411600-39413400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr19:39411600-39413400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:39411600-39413600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr19:39411600-39417000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr19:39411600-39420400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:39411600-39420400	Weak transcription	Fetal Heart	heart
44	chr19:39411800-39413600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr19:39411800-39413600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr19:39411800-39417200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr19:39412000-39413400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:39412000-39413400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr19:39412000-39413400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:39412000-39413400	Strong transcription	Gastric	stomach

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