Variant report

Variant	rs4802998
Chromosome Location	chr19:39387716-39387717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39387225..39388812-chr19:39419975..39421625,2	K562	blood:
2	chr19:39370094..39372680-chr19:39385555..39388112,2	K562	blood:
3	chr19:39386472..39392494-chr19:39418718..39424791,9	K562	blood:
4	chr19:39372814..39374883-chr19:39387174..39390098,2	K562	blood:
5	chr19:39289769..39291499-chr19:39387301..39389703,2	K562	blood:
6	chr19:39296580..39299449-chr19:39386165..39387778,2	K562	blood:
7	chr19:39378309..39379835-chr19:39385116..39387843,2	K562	blood:
8	chr19:39338478..39344219-chr19:39387112..39393304,19	K562	blood:
9	chr19:39340275..39343008-chr19:39385352..39388612,4	K562	blood:
10	chr19:39378605..39380254-chr19:39386425..39388903,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128626	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000171747	Chromatin interaction
ENSG00000068903	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10410544	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10416055	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10426382	1.00[JPT][hapmap]
rs10775533	0.92[ASN][1000 genomes]
rs11083485	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11083489	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11668245	0.92[ASN][1000 genomes]
rs12462710	0.92[ASN][1000 genomes]
rs12610409	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972925	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12972986	0.92[ASN][1000 genomes]
rs12979755	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17545254	0.92[ASN][1000 genomes]
rs1808662	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1865047	0.85[ASN][1000 genomes]
rs2278412	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs3136640	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801960	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4801971	0.92[ASN][1000 genomes]
rs4803006	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803034	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs575	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6508814	1.00[JPT][hapmap]
rs7257007	0.92[ASN][1000 genomes]
rs730078	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7508411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7508539	0.92[ASN][1000 genomes]
rs8113389	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9636109	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4802998	GPR4	cis	parietal	SCAN
rs4802998	LGALS14	cis	parietal	SCAN
rs4802998	MYPOP	cis	parietal	SCAN
rs4802998	SARS2	cis	multi-tissue	Pritchard
rs4802998	SARS2	cis	lymphoblastoid	seeQTL
rs4802998	PLD3	cis	parietal	SCAN
rs4802998	CTC-360G5.9	cis	Nerve Tibial	GTEx
rs4802998	ZNF285	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39369200-39389200	Weak transcription	A549	lung
2	chr19:39369400-39388800	Weak transcription	Stomach Mucosa	stomach
3	chr19:39371600-39389800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:39372400-39388800	Weak transcription	Fetal Kidney	kidney
5	chr19:39377200-39388600	Weak transcription	K562	blood
6	chr19:39379800-39388600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:39379800-39389000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:39380000-39388400	Weak transcription	HMEC	breast
9	chr19:39380000-39388800	Weak transcription	NHDF-Ad	bronchial
10	chr19:39380000-39389400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:39380000-39389400	Weak transcription	NH-A	brain
12	chr19:39380200-39388800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:39380200-39389000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:39380200-39389000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:39380200-39389000	Weak transcription	HUVEC	blood vessel
16	chr19:39380200-39389000	Weak transcription	Osteobl	bone
17	chr19:39380400-39388600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:39380400-39388800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr19:39380400-39388800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr19:39380400-39389000	Weak transcription	Small Intestine	intestine
21	chr19:39380600-39388600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:39380600-39388800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr19:39380600-39389000	Weak transcription	Colonic Mucosa	Colon
24	chr19:39380800-39388200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:39381000-39388600	Weak transcription	Pancreas	Pancrea
26	chr19:39381200-39388400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:39381200-39388600	Weak transcription	NHLF	lung
28	chr19:39381200-39389000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr19:39381400-39389000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:39381600-39387800	Weak transcription	HepG2	liver
31	chr19:39381600-39388800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:39381600-39389000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:39381600-39389000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:39381600-39389200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:39381800-39387800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:39381800-39387800	Weak transcription	Dnd41	blood
37	chr19:39381800-39388200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr19:39381800-39388600	Weak transcription	NHEK	skin
39	chr19:39381800-39389000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:39382000-39388600	Weak transcription	Liver	Liver
41	chr19:39382000-39388800	Weak transcription	Esophagus	oesophagus
42	chr19:39382000-39389000	Weak transcription	Primary B cells from cord blood	blood
43	chr19:39382000-39389600	Weak transcription	Aorta	Aorta
44	chr19:39382400-39389200	Weak transcription	Primary T cells from cord blood	blood
45	chr19:39382800-39388600	Weak transcription	Gastric	stomach
46	chr19:39383400-39388600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:39383800-39388600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:39383800-39388800	Enhancers	Brain Substantia Nigra	brain
49	chr19:39384200-39388600	Weak transcription	Fetal Lung	lung
50	chr19:39384200-39388800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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