Variant report

Variant	rs10402813
Chromosome Location	chr19:39449411-39449412
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10415953	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416101	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880780	1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[ASN][1000 genomes]
rs12979835	0.83[ASN][1000 genomes]
rs7248334	0.88[ASN][1000 genomes]
rs9676853	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv2762038	chr19:39444417-39455548	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10402813	FBXO27	cis	Esophagus Mucosa	GTEx
rs10402813	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs10402813	ZNF428	cis	cerebellum	SCAN
rs10402813	PLD3	cis	parietal	SCAN

Chromatin state (count:58 , 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	chr19:39438400-39453000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr19:39439200-39452600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:39441000-39453000	Weak transcription	Aorta	Aorta
6	chr19:39441000-39459200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:39441200-39450400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:39441200-39452800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr19:39441200-39453000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:39441200-39453000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:39441200-39453000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:39441200-39453000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:39441200-39453000	Weak transcription	Brain Hippocampus Middle	brain
14	chr19:39441200-39453000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:39441200-39453000	Weak transcription	Lung	lung
16	chr19:39441200-39453000	Weak transcription	Pancreas	Pancrea
17	chr19:39441200-39453000	Weak transcription	Osteobl	bone
18	chr19:39441200-39455800	Weak transcription	Psoas Muscle	Psoas
19	chr19:39441200-39459400	Weak transcription	Fetal Lung	lung
20	chr19:39441200-39465200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:39441200-39465200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:39441200-39465200	Weak transcription	NHLF	lung
23	chr19:39441200-39465400	Weak transcription	Right Atrium	heart
24	chr19:39441400-39452600	Weak transcription	Adipose Nuclei	Adipose
25	chr19:39441400-39452600	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:39441400-39453000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:39441400-39453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:39441400-39453000	Weak transcription	Fetal Brain Male	brain
29	chr19:39441400-39453000	Weak transcription	Fetal Brain Female	brain
30	chr19:39441400-39453000	Weak transcription	Ovary	ovary
31	chr19:39441400-39453000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr19:39441400-39453200	Weak transcription	Fetal Heart	heart
33	chr19:39441400-39462000	Weak transcription	Small Intestine	intestine
34	chr19:39441400-39465000	Weak transcription	HUVEC	blood vessel
35	chr19:39441600-39450200	Strong transcription	Fetal Stomach	stomach
36	chr19:39443400-39453000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr19:39443600-39452800	Weak transcription	Fetal Kidney	kidney
38	chr19:39443600-39453000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr19:39443600-39453000	Weak transcription	HSMM	muscle
40	chr19:39444600-39452200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr19:39444800-39450200	Weak transcription	HepG2	liver
42	chr19:39445000-39453000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:39445000-39453000	Weak transcription	Liver	Liver
44	chr19:39445800-39453000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr19:39446000-39449600	Strong transcription	A549	lung
46	chr19:39446200-39449800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:39446200-39453000	Strong transcription	Fetal Intestine Small	intestine
48	chr19:39446800-39455400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:39447200-39449800	Strong transcription	Fetal Muscle Leg	muscle
50	chr19:39447600-39449800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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