Variant report

Variant	rs3745951
Chromosome Location	chr19:38817486-38817487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38815734..38818245-chr19:38825001..38828035,3	K562	blood:
2	chr19:38810442..38812628-chr19:38816894..38818676,3	K562	blood:
3	chr19:38759354..38761774-chr19:38815692..38818427,2	K562	blood:
4	chr19:38815734..38817911-chr19:38825001..38827555,2	K562	blood:

Variant related genes	Relation type
ENSG00000099337	Chromatin interaction
ENSG00000099338	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11668355	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11668651	0.85[ASN][1000 genomes]
rs11669131	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11669230	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11671779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11672219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11672531	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]
rs11672793	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11673012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11673222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12459746	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs2270093	0.89[EUR][1000 genomes]
rs2270094	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2270095	0.84[CEU][hapmap]
rs2286475	0.84[CEU][hapmap]
rs2286476	0.84[CEU][hapmap]
rs2302182	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2302183	0.87[ASN][1000 genomes]
rs2304176	0.84[CEU][hapmap]
rs2304177	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2368484	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2887262	0.87[AMR][1000 genomes]
rs34989303	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35308902	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3745952	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816044	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs4386247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45437199	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802326	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4802327	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4802351	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs4804016	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4804046	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60082376	0.88[ASN][1000 genomes]
rs73041302	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8101488	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8104823	0.87[MEX][hapmap]
rs8106900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8112211	0.84[CEU][hapmap]
rs870218	0.87[MEX][hapmap]
rs931749	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs931750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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
rs3745951	APOC4	cis	cerebellum	SCAN
rs3745951	C19orf33	cis	normal skin	skin_eQTL
rs3745951	KCNK6	cis	multi-tissue	Pritchard
rs3745951	PPP1R14A	cis	multi-tissue	Pritchard
rs3745951	C19orf33	cis	multi-tissue	Pritchard
rs3745951	CYP2S1	cis	cerebellum	SCAN
rs3745951	SELV	cis	parietal	SCAN
rs3745951	KCNK6	cis	lymphoblastoid	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38811200-38817600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:38811200-38817600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr19:38811200-38826200	Weak transcription	Brain Anterior Caudate	brain
4	chr19:38811200-38826600	Weak transcription	Brain Substantia Nigra	brain
5	chr19:38811400-38825600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr19:38811600-38819800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:38811800-38823000	Weak transcription	Brain Angular Gyrus	brain
8	chr19:38812000-38826000	Weak transcription	Fetal Thymus	thymus
9	chr19:38812000-38826600	Weak transcription	HUVEC	blood vessel
10	chr19:38812200-38817800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:38812200-38823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr19:38812200-38826400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:38812200-38826600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:38812400-38817600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:38812400-38817600	Weak transcription	Left Ventricle	heart
16	chr19:38812400-38826400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr19:38812400-38826400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:38812400-38826400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr19:38812600-38817600	Weak transcription	Brain Hippocampus Middle	brain
20	chr19:38812600-38817600	Weak transcription	Fetal Muscle Leg	muscle
21	chr19:38812600-38818200	Weak transcription	HSMM	muscle
22	chr19:38812600-38826200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:38813000-38818000	Weak transcription	Fetal Lung	lung
24	chr19:38813000-38818200	Weak transcription	HSMMtube	muscle
25	chr19:38813000-38826000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:38813000-38826400	Weak transcription	Stomach Mucosa	stomach
27	chr19:38813200-38826800	Weak transcription	Fetal Heart	heart
28	chr19:38813400-38826000	Weak transcription	Fetal Intestine Large	intestine
29	chr19:38813800-38819200	Strong transcription	Primary T cells from cord blood	blood
30	chr19:38814000-38819400	Strong transcription	Fetal Stomach	stomach
31	chr19:38814000-38819600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr19:38814000-38820600	Strong transcription	Aorta	Aorta
33	chr19:38814000-38826400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr19:38814200-38817600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:38814200-38818800	Weak transcription	K562	blood
36	chr19:38814200-38820600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:38814200-38826400	Weak transcription	Right Atrium	heart
38	chr19:38814400-38819200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:38814400-38819400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr19:38814600-38820000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:38814600-38822800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:38814600-38826400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:38814800-38819400	Strong transcription	Osteobl	bone
44	chr19:38814800-38820400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr19:38815000-38818800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr19:38815000-38819000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:38815000-38819000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:38815000-38819000	Strong transcription	Colon Smooth Muscle	Colon
49	chr19:38815000-38819200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr19:38815000-38819200	Strong transcription	Fetal Intestine Small	intestine

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