Variant report

Variant	rs8100824
Chromosome Location	chr19:18749412-18749413
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18746749..18750617-chr19:18752436..18756057,4	K562	blood:
2	chr19:18703681..18707981-chr19:18746387..18750076,5	K562	blood:
3	chr19:18681104..18684544-chr19:18745683..18749906,4	K562	blood:
4	chr19:18698512..18700358-chr19:18745222..18750244,4	K562	blood:
5	chr19:18630375..18633112-chr19:18747617..18750132,3	K562	blood:

Variant related genes	Relation type
ENSG00000006015	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000167487	Chromatin interaction
ENSG00000006016	Chromatin interaction
ENSG00000105656	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10221489	0.85[CHB][hapmap]
rs10412053	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10412858	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10419226	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10420228	0.83[ASN][1000 genomes]
rs10421503	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10423674	0.85[CHB][hapmap]
rs10424265	0.85[ASN][1000 genomes]
rs10854003	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11085236	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883401	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12976113	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473116	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[ASN][1000 genomes]
rs1991017	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs2214524	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2385178	0.85[ASN][1000 genomes]
rs3764627	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3829671	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808147	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6510995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6510996	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7246437	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7257812	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757347	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757350	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8102046	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs876982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs886443	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs889364	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	esv3332947	chr19:18745902-18749700	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv1849639	chr19:18747006-18780799	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8100824	UBA52	cis	lymphoblastoid	seeQTL
rs8100824	UNC13A	cis	parietal	SCAN
rs8100824	GDF1	cis	parietal	SCAN
rs8100824	UBA52	trans	brain	seeQTL
rs8100824	CRLF1	cis	cerebellum	SCAN
rs8100824	UBA52	cis	multi-tissue	Pritchard
rs8100824	UBA52	cis	brain	seeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18748400-18749800	Enhancers	Spleen	Spleen
2	chr19:18748400-18761600	Weak transcription	Aorta	Aorta
3	chr19:18748600-18749600	Enhancers	Fetal Intestine Small	intestine
4	chr19:18748600-18755800	Weak transcription	Ovary	ovary
5	chr19:18748600-18774400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:18748800-18749600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:18748800-18749800	Enhancers	Pancreas	Pancrea
8	chr19:18748800-18751000	Weak transcription	Fetal Stomach	stomach
9	chr19:18748800-18754800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:18748800-18757400	Weak transcription	Fetal Kidney	kidney
11	chr19:18748800-18758600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:18748800-18759200	Weak transcription	Fetal Lung	lung
13	chr19:18749000-18749600	Enhancers	Primary T cells from cord blood	blood
14	chr19:18749000-18749800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr19:18749000-18750400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:18749000-18750600	Weak transcription	Fetal Muscle Leg	muscle
17	chr19:18749000-18751000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr19:18749000-18751800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:18749000-18755200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr19:18749000-18755400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:18749200-18749800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:18749200-18749800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr19:18749200-18749800	Enhancers	Duodenum Mucosa	Duodenum
24	chr19:18749200-18750800	Enhancers	Colon Smooth Muscle	Colon
25	chr19:18749200-18754600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr19:18749200-18754600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:18749200-18754800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr19:18749200-18754800	Weak transcription	Brain Substantia Nigra	brain
29	chr19:18749200-18754800	Weak transcription	NHLF	lung
30	chr19:18749200-18754800	Weak transcription	Osteobl	bone
31	chr19:18749200-18755000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:18749200-18755000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:18749200-18755000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr19:18749200-18755200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr19:18749200-18756200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr19:18749200-18757200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:18749200-18757400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:18749200-18757600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:18749200-18759000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:18749200-18759600	Weak transcription	Thymus	Thymus
41	chr19:18749200-18759800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:18749200-18768200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:18749200-18778400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr19:18749400-18749600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:18749400-18749600	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr19:18749400-18749800	Enhancers	Dnd41	blood
47	chr19:18749400-18750400	Weak transcription	Psoas Muscle	Psoas
48	chr19:18749400-18750600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:18749400-18751000	Weak transcription	Stomach Mucosa	stomach
50	chr19:18749400-18752600	Weak transcription	Hela-S3	cervix

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