Variant report

Variant	rs4802086
Chromosome Location	chr19:41230146-41230147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41225203..41228152-chr19:41229042..41232599,3	MCF-7	breast:
2	chr19:41228463..41230519-chr19:41256457..41258245,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077312	Chromatin interaction
ENSG00000188493	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10407351	0.85[ASN][1000 genomes]
rs10425765	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083566	0.86[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]
rs11548478	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12976551	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1469427	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1870086	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs1870087	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs2246095	0.90[JPT][hapmap]
rs2288451	0.90[JPT][hapmap]
rs2290692	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]
rs2290693	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2369302	0.81[JPT][hapmap]
rs2604882	0.81[JPT][hapmap]
rs2604885	0.90[JPT][hapmap]
rs3745210	0.88[ASN][1000 genomes]
rs3745211	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745216	0.95[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3865452	0.81[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes]
rs4802085	0.83[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs4802087	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803358	0.82[EUR][1000 genomes]
rs7248468	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7248570	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7251246	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257602	0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs7260405	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8111960	0.86[CEU][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4802086	C19orf54	Cis_1M	lymphoblastoid	RTeQTL
rs4802086	ADCK4	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41225200-41235200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41225200-41238800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41225200-41243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:41225400-41231000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr19:41225600-41231600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr19:41225800-41232000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:41225800-41232200	Weak transcription	Fetal Kidney	kidney
8	chr19:41225800-41233400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr19:41225800-41233400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr19:41225800-41236400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:41226400-41246200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:41226600-41238600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr19:41226600-41245600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:41226800-41236600	Weak transcription	GM12878-XiMat	blood
15	chr19:41226800-41245200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:41226800-41245600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:41226800-41245800	Strong transcription	Fetal Stomach	stomach
18	chr19:41227000-41254600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr19:41227200-41231000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:41227200-41231000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:41227200-41231200	Weak transcription	Aorta	Aorta
22	chr19:41227200-41232200	Weak transcription	K562	blood
23	chr19:41227200-41237000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr19:41227200-41255200	Weak transcription	Fetal Heart	heart
25	chr19:41227800-41230600	Genic enhancers	Stomach Smooth Muscle	stomach
26	chr19:41228000-41231000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:41228000-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:41228200-41231800	Strong transcription	Fetal Thymus	thymus
29	chr19:41228200-41238000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr19:41228200-41241400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr19:41228200-41246600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr19:41228200-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:41228400-41234000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:41228600-41231000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:41228600-41231000	Weak transcription	Brain Hippocampus Middle	brain
36	chr19:41228600-41231000	Weak transcription	Colonic Mucosa	Colon
37	chr19:41228600-41232000	Weak transcription	Small Intestine	intestine
38	chr19:41228600-41232200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr19:41228600-41232400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr19:41228600-41233400	Weak transcription	Psoas Muscle	Psoas
41	chr19:41228600-41236000	Weak transcription	Fetal Brain Male	brain
42	chr19:41228600-41236400	Weak transcription	NHDF-Ad	bronchial
43	chr19:41228600-41237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:41228600-41238800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:41228600-41240000	Weak transcription	Stomach Mucosa	stomach
46	chr19:41228600-41240400	Strong transcription	HepG2	liver
47	chr19:41228600-41241200	Strong transcription	A549	lung
48	chr19:41228600-41245400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr19:41228600-41245600	Strong transcription	Fetal Muscle Leg	muscle
50	chr19:41228600-41250000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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