Variant report

Variant	rs1865047
Chromosome Location	chr19:39437534-39437535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39437379-39437819	K562	blood:	n/a	n/a
2	REST	chr19:39436440-39437766	PANC-1	pancreas:	n/a	n/a
3	REST	chr19:39436586-39437916	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:39436715-39441620	PANC-1	pancreas:	n/a	n/a
5	REST	chr19:39436514-39437751	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:39437094-39437678	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:39428415-39444124	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:39432173-39442255	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:39436667-39437960	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39421083..39425618-chr19:39435632..39441753,7	MCF-7	breast:

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

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10416055	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425217	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10775533	0.92[ASN][1000 genomes]
rs11083485	0.81[ASN][1000 genomes]
rs11083489	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11668245	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12462710	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12610409	0.85[ASN][1000 genomes]
rs12972925	0.86[ASN][1000 genomes]
rs12972986	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12979755	0.85[ASN][1000 genomes]
rs12982957	0.86[EUR][1000 genomes]
rs17545254	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1808661	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1808662	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1865049	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3136640	0.85[ASN][1000 genomes]
rs4801971	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802998	0.85[ASN][1000 genomes]
rs4803006	0.85[ASN][1000 genomes]
rs4803034	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs575	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7257007	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs730078	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7508411	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7508539	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8113389	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9636109	0.85[ASN][1000 genomes]
rs9749516	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1865047	CTC-360G5.9	cis	Nerve Tibial	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422400-39440600	Weak transcription	NHDF-Ad	bronchial
2	chr19:39422600-39440200	Weak transcription	NH-A	brain
3	chr19:39422600-39440600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
5	chr19:39423200-39440800	Weak transcription	Fetal Heart	heart
6	chr19:39423600-39440400	Weak transcription	Right Atrium	heart
7	chr19:39423600-39440600	Weak transcription	Gastric	stomach
8	chr19:39424400-39440000	Weak transcription	Fetal Brain Female	brain
9	chr19:39424600-39440200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr19:39424600-39440200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:39424800-39440200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:39424800-39440200	Weak transcription	Brain Substantia Nigra	brain
13	chr19:39425400-39440400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:39425600-39440200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr19:39425800-39440200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:39425800-39440600	Weak transcription	Esophagus	oesophagus
17	chr19:39425800-39440600	Weak transcription	Left Ventricle	heart
18	chr19:39425800-39440600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr19:39425800-39440600	Weak transcription	Right Ventricle	heart
20	chr19:39425800-39440600	Weak transcription	NHEK	skin
21	chr19:39426000-39440200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr19:39426400-39440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:39431400-39440200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr19:39431400-39440600	Weak transcription	HUVEC	blood vessel
25	chr19:39431600-39439600	Strong transcription	Fetal Muscle Leg	muscle
26	chr19:39431800-39440200	Strong transcription	Fetal Intestine Small	intestine
27	chr19:39432000-39440200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr19:39432200-39440200	Strong transcription	Fetal Stomach	stomach
29	chr19:39432400-39439600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr19:39432400-39441800	Strong transcription	A549	lung
31	chr19:39432600-39440200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:39432800-39440200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:39432800-39440800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr19:39433200-39438600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr19:39433200-39439600	Strong transcription	Liver	Liver
36	chr19:39433400-39440600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:39433600-39440200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr19:39433600-39440600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:39433800-39440200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:39434000-39439200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr19:39434400-39438200	Strong transcription	Ovary	ovary
42	chr19:39434400-39439200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:39434400-39439200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:39434400-39440000	Strong transcription	Fetal Intestine Large	intestine
45	chr19:39434600-39437800	Strong transcription	Colon Smooth Muscle	Colon
46	chr19:39434600-39438400	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr19:39434600-39439200	Strong transcription	Stomach Smooth Muscle	stomach
48	chr19:39435000-39438800	Strong transcription	Fetal Lung	lung
49	chr19:39435000-39439200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:39435000-39439200	Strong transcription	Adipose Nuclei	Adipose

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