Variant report

Variant	rs4312417
Chromosome Location	chr19:38797189-38797190
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38753031..38764322-chr19:38787496..38798494,54	MCF-7	breast:
2	chr19:38718266..38721870-chr19:38794040..38798765,4	MCF-7	breast:
3	chr19:38779327..38783351-chr19:38794485..38798006,3	K562	blood:
4	chr19:38793982..38798570-chr19:38826004..38829304,4	K562	blood:
5	chr19:38795298..38801659-chr19:38801673..38807893,10	K562	blood:
6	chr19:38744545..38747881-chr19:38796739..38799856,3	K562	blood:
7	chr19:38395819..38398093-chr19:38795612..38797644,2	MCF-7	breast:
8	chr19:38796381..38798650-chr19:38799992..38801610,2	K562	blood:
9	chr19:38776349..38778881-chr19:38795381..38797610,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000167645	Chromatin interaction
ENSG00000267748	Chromatin interaction
ENSG00000167641	Chromatin interaction
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000167642	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11880532	0.83[YRI][hapmap]
rs11881305	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12609247	0.83[MEX][hapmap]
rs12611255	0.83[AMR][1000 genomes]
rs1821284	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2270095	0.86[ASW][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap]
rs2286475	0.89[GIH][hapmap];0.95[TSI][hapmap]
rs2286476	0.81[CEU][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap]
rs2304176	0.91[GIH][hapmap];0.97[TSI][hapmap]
rs3178327	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35436012	0.86[EUR][1000 genomes]
rs3843754	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4802324	1.00[ASW][hapmap];0.83[CEU][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4803999	0.83[EUR][1000 genomes]
rs61160177	0.83[AMR][1000 genomes]
rs71354995	0.93[EUR][1000 genomes]
rs7253960	0.83[AMR][1000 genomes]
rs7257537	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7260137	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8112211	0.91[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv960928	chr19:38790012-38822380	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4312417	C19orf33	cis	multi-tissue	Pritchard
rs4312417	C19orf33	cis	uninvolved skin	skin_eQTL
rs4312417	PPP1R14A	cis	multi-tissue	Pritchard
rs4312417	PSG4	cis	cerebellum	SCAN
rs4312417	SELV	cis	parietal	SCAN
rs4312417	C19orf33	cis	normal skin	skin_eQTL
rs4312417	APOC4	cis	cerebellum	SCAN
rs4312417	C19orf33	cis	lesional skin	skin_eQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38771400-38805800	Weak transcription	Right Atrium	heart
2	chr19:38781200-38805800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:38781400-38797800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr19:38782000-38806000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:38782400-38798000	Weak transcription	Fetal Thymus	thymus
6	chr19:38784000-38797200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr19:38784000-38805800	Weak transcription	Primary B cells from cord blood	blood
8	chr19:38790000-38797800	Weak transcription	Ovary	ovary
9	chr19:38791600-38798000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:38791800-38797600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr19:38791800-38797800	Weak transcription	HSMMtube	muscle
12	chr19:38791800-38797800	Weak transcription	Osteobl	bone
13	chr19:38791800-38798000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:38792000-38797600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:38792000-38805400	Weak transcription	NHDF-Ad	bronchial
16	chr19:38792000-38805800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:38793400-38797600	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:38794400-38797200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:38794400-38800200	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr19:38794400-38800400	Strong transcription	Aorta	Aorta
21	chr19:38794400-38800400	Strong transcription	Thymus	Thymus
22	chr19:38794400-38800400	Strong transcription	NHLF	lung
23	chr19:38794600-38799400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:38794800-38799600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:38794800-38800400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:38795000-38797200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:38795200-38797800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr19:38795200-38800600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:38795200-38805800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:38795400-38797600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:38795400-38797600	Weak transcription	Small Intestine	intestine
32	chr19:38795400-38797800	Weak transcription	Left Ventricle	heart
33	chr19:38795400-38800000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr19:38795400-38800200	Strong transcription	Brain Germinal Matrix	brain
35	chr19:38795400-38800400	Strong transcription	Dnd41	blood
36	chr19:38795400-38800600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr19:38795400-38800600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:38795400-38805800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:38795600-38797800	Weak transcription	Gastric	stomach
40	chr19:38795600-38798200	Weak transcription	HSMM	muscle
41	chr19:38795600-38798600	Weak transcription	Fetal Lung	lung
42	chr19:38795600-38798800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr19:38795600-38799000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr19:38795600-38800800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr19:38795600-38805800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr19:38795800-38797800	Weak transcription	Brain Angular Gyrus	brain
47	chr19:38795800-38798000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr19:38795800-38798000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:38795800-38800800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:38795800-38801800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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