Variant report

Variant	rs3178327
Chromosome Location	chr19:38798086-38798087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr19:38793982..38798570-chr19:38826004..38829304,4	K562	blood:
4	chr19:38795298..38801659-chr19:38801673..38807893,10	K562	blood:
5	chr19:38744545..38747881-chr19:38796739..38799856,3	K562	blood:
6	chr19:38780526..38782372-chr19:38797679..38799619,2	K562	blood:
7	chr19:38796381..38798650-chr19:38799992..38801610,2	K562	blood:

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

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11881305	1.00[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12609247	0.85[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs12611255	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1821284	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2270095	0.95[GIH][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap]
rs2286475	0.95[GIH][hapmap];0.95[TSI][hapmap]
rs2286476	0.81[CEU][hapmap];0.93[GIH][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap]
rs2304176	0.98[GIH][hapmap];0.97[TSI][hapmap]
rs35436012	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3843754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4312417	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]
rs4802324	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803999	0.84[EUR][1000 genomes]
rs61160177	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71354995	0.95[EUR][1000 genomes]
rs7253960	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7257537	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7260137	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8112211	0.81[ASW][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.89[MKK][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3178327	SELV	cis	parietal	SCAN
rs3178327	C19orf33	cis	normal skin	skin_eQTL
rs3178327	C19orf33	cis	Nerve Tibial	GTEx
rs3178327	C19orf33	cis	lesional skin	skin_eQTL
rs3178327	APOC4	cis	cerebellum	SCAN
rs3178327	PSG4	cis	cerebellum	SCAN
rs3178327	C19orf33	cis	uninvolved 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	chr19:38782000-38806000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:38784000-38805800	Weak transcription	Primary B cells from cord blood	blood
5	chr19:38792000-38805400	Weak transcription	NHDF-Ad	bronchial
6	chr19:38792000-38805800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:38794400-38800200	Strong transcription	Brain Inferior Temporal Lobe	brain
8	chr19:38794400-38800400	Strong transcription	Aorta	Aorta
9	chr19:38794400-38800400	Strong transcription	Thymus	Thymus
10	chr19:38794400-38800400	Strong transcription	NHLF	lung
11	chr19:38794600-38799400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:38794800-38799600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:38794800-38800400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:38795200-38800600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:38795200-38805800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr19:38795400-38800000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr19:38795400-38800200	Strong transcription	Brain Germinal Matrix	brain
18	chr19:38795400-38800400	Strong transcription	Dnd41	blood
19	chr19:38795400-38800600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:38795400-38800600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:38795400-38805800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:38795600-38798200	Weak transcription	HSMM	muscle
23	chr19:38795600-38798600	Weak transcription	Fetal Lung	lung
24	chr19:38795600-38798800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr19:38795600-38799000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr19:38795600-38800800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr19:38795600-38805800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr19:38795800-38800800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:38795800-38801800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:38796000-38800400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:38796000-38800400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:38796000-38800400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:38796000-38803400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:38796200-38798400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:38796200-38798400	Weak transcription	GM12878-XiMat	blood
36	chr19:38796200-38800000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr19:38796200-38800200	Strong transcription	Liver	Liver
38	chr19:38796200-38804400	Weak transcription	NH-A	brain
39	chr19:38796200-38805400	Weak transcription	HepG2	liver
40	chr19:38796400-38798400	Weak transcription	K562	blood
41	chr19:38796400-38799200	Strong transcription	Lung	lung
42	chr19:38796400-38800200	Strong transcription	Fetal Muscle Leg	muscle
43	chr19:38796400-38800400	Strong transcription	Adipose Nuclei	Adipose
44	chr19:38796400-38800800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr19:38796400-38801600	Strong transcription	Fetal Stomach	stomach
46	chr19:38796400-38801800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:38796400-38803200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr19:38796400-38805400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:38796400-38805600	Weak transcription	Hela-S3	cervix
50	chr19:38796400-38805800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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