Variant report

Variant	rs2290692
Chromosome Location	chr19:41246378-41246379
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41221453..41223468-chr19:41246365..41247883,2	MCF-7	breast:
2	chr19:41222847..41224765-chr19:41244850..41247375,2	MCF-7	breast:
3	chr19:41237106..41239514-chr19:41244593..41247355,2	K562	blood:
4	chr19:41222621..41224327-chr19:41244939..41247313,2	K562	blood:
5	chr19:41167265..41169750-chr19:41244881..41246475,2	K562	blood:
6	chr19:41246355..41251647-chr19:41252986..41257062,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000077312	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10407351	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425765	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11083566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11548478	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976551	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1469427	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1870086	0.96[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1870087	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2115239	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2246095	0.91[JPT][hapmap]
rs2288451	0.88[CEU][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs2290693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2369302	0.82[JPT][hapmap]
rs2604885	0.91[JPT][hapmap]
rs3745210	0.90[ASN][1000 genomes]
rs3745211	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745216	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3865452	0.91[JPT][hapmap]
rs4802085	0.96[CEU][hapmap];0.91[JPT][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4802086	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802087	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803360	0.85[EUR][1000 genomes]
rs7248468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7251246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7257602	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7260405	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111960	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs890934	0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2290692	C19orf54	cis	Nerve Tibial	GTEx
rs2290692	ADCK4	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41227000-41254600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr19:41227200-41255200	Weak transcription	Fetal Heart	heart
3	chr19:41228000-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:41228200-41246600	Strong transcription	Primary B cells from peripheral blood	blood
5	chr19:41228200-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:41228600-41250000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:41228600-41251000	Strong transcription	Fetal Brain Female	brain
8	chr19:41229200-41246800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:41229200-41247200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:41229400-41246800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:41229400-41246800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr19:41229400-41249000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:41229600-41246800	Strong transcription	Fetal Lung	lung
14	chr19:41229800-41246400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr19:41229800-41246800	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr19:41229800-41247000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:41229800-41247000	Strong transcription	Liver	Liver
18	chr19:41229800-41247200	Strong transcription	Primary T cells from cord blood	blood
19	chr19:41229800-41248600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:41229800-41248600	Strong transcription	Dnd41	blood
21	chr19:41229800-41249200	Strong transcription	Thymus	Thymus
22	chr19:41229800-41250400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr19:41230200-41247000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr19:41230400-41246600	Strong transcription	Left Ventricle	heart
25	chr19:41230400-41247200	Strong transcription	Lung	lung
26	chr19:41231600-41247000	Strong transcription	Pancreas	Pancrea
27	chr19:41231600-41247400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:41232400-41247400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr19:41233200-41246600	Strong transcription	Fetal Thymus	thymus
30	chr19:41233400-41246400	Strong transcription	Brain Germinal Matrix	brain
31	chr19:41233600-41248400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:41233600-41249200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr19:41234800-41248400	Strong transcription	Gastric	stomach
34	chr19:41237000-41255400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:41237600-41255200	Weak transcription	Fetal Brain Male	brain
36	chr19:41238800-41248000	Strong transcription	Primary B cells from cord blood	blood
37	chr19:41239000-41246800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr19:41239400-41250000	Strong transcription	Spleen	Spleen
39	chr19:41240000-41247000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr19:41240200-41255600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr19:41241600-41251000	Weak transcription	NH-A	brain
42	chr19:41241800-41248800	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr19:41242000-41247200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:41242000-41248000	Strong transcription	HepG2	liver
45	chr19:41242000-41250600	Strong transcription	Fetal Intestine Small	intestine
46	chr19:41242000-41253800	Weak transcription	GM12878-XiMat	blood
47	chr19:41242200-41255600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr19:41242400-41246400	Strong transcription	A549	lung
49	chr19:41242400-41246600	Strong transcription	HMEC	breast
50	chr19:41242400-41251000	Weak transcription	Hela-S3	cervix

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