Variant report

Variant	rs833895
Chromosome Location	chr19:38470653-38470654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38469123..38470666-chr19:38472308..38474390,3	MCF-7	breast:
2	chr19:38421146..38425969-chr19:38469812..38473788,8	MCF-7	breast:
3	chr19:38470130..38474074-chr19:38479565..38484723,5	MCF-7	breast:
4	chr19:38429570..38433364-chr19:38470420..38473384,4	MCF-7	breast:
5	chr19:38459331..38461760-chr19:38470604..38472306,2	MCF-7	breast:
6	chr19:38395951..38398517-chr19:38469657..38472006,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10404567	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs10415548	0.83[CEU][hapmap]
rs10420746	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1119229	0.87[CEU][hapmap]
rs1643462	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1643463	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1643466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1643467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1643468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1643469	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1725469	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1725477	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725478	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725480	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725482	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725483	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725485	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725487	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725488	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1725494	0.90[EUR][1000 genomes]
rs1725499	0.83[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2544718	0.90[EUR][1000 genomes]
rs35209753	0.80[EUR][1000 genomes]
rs353398	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353399	0.93[EUR][1000 genomes]
rs353400	0.93[EUR][1000 genomes]
rs353402	0.93[EUR][1000 genomes]
rs353403	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs353404	0.93[EUR][1000 genomes]
rs353407	0.93[EUR][1000 genomes]
rs353410	0.83[CEU][hapmap]
rs353411	0.83[CEU][hapmap]
rs353414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353415	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs353416	0.93[EUR][1000 genomes]
rs353417	0.93[EUR][1000 genomes]
rs353419	0.93[EUR][1000 genomes]
rs353420	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353421	0.93[EUR][1000 genomes]
rs353423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353424	0.93[EUR][1000 genomes]
rs353425	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353426	0.91[EUR][1000 genomes]
rs353427	0.93[EUR][1000 genomes]
rs353428	0.88[EUR][1000 genomes]
rs353429	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs353430	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3786869	0.82[CEU][hapmap]
rs4239516	0.83[CEU][hapmap]
rs4802135	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4803524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4803551	0.87[CEU][hapmap]
rs4803573	0.87[CEU][hapmap]
rs705491	0.87[CEU][hapmap]
rs705492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs705493	0.87[CEU][hapmap]
rs705494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs705495	0.87[CEU][hapmap]
rs705500	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs7258597	0.82[EUR][1000 genomes]
rs752878	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs8107341	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs8113521	0.83[CEU][hapmap]
rs833896	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs833897	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833898	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833914	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs833926	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9304572	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs833895	ZNF571	cis	multi-tissue	Pritchard
rs833895	WDR87	cis	Thyroid	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38461600-38472000	Weak transcription	NHDF-Ad	bronchial
2	chr19:38461600-38476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr19:38461800-38476800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:38462200-38470800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:38462200-38471800	Enhancers	Primary B cells from peripheral blood	blood
8	chr19:38463600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
11	chr19:38466000-38472400	Weak transcription	Primary T cells from cord blood	blood
12	chr19:38466000-38475800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:38467800-38471800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr19:38468000-38472000	Enhancers	Primary B cells from cord blood	blood
15	chr19:38468200-38471200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:38468200-38473600	Enhancers	Lung	lung
17	chr19:38468200-38474200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:38468200-38474600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:38468200-38475600	Enhancers	HMEC	breast
20	chr19:38468200-38475800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:38468200-38483600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr19:38468400-38473000	Enhancers	NH-A	brain
23	chr19:38468400-38473200	Enhancers	HSMM	muscle
24	chr19:38468800-38474000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:38469000-38471200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr19:38469000-38474200	Enhancers	Fetal Intestine Large	intestine
27	chr19:38469200-38471200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr19:38469200-38471400	Weak transcription	Osteobl	bone
29	chr19:38469200-38474800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:38469200-38479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:38469400-38471000	Weak transcription	Fetal Kidney	kidney
32	chr19:38469800-38475800	Genic enhancers	Fetal Intestine Small	intestine
33	chr19:38470000-38472800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr19:38470200-38470800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:38470200-38470800	Flanking Active TSS	HepG2	liver
36	chr19:38470200-38471000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr19:38470200-38471000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:38470200-38471400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:38470200-38471400	Flanking Active TSS	GM12878-XiMat	blood
40	chr19:38470200-38472000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:38470200-38472200	Enhancers	Duodenum Mucosa	Duodenum
42	chr19:38470200-38472200	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr19:38470200-38472600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:38470200-38473200	Enhancers	Fetal Lung	lung
45	chr19:38470200-38474200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr19:38470200-38474200	Enhancers	Stomach Mucosa	stomach
47	chr19:38470200-38474400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr19:38470400-38470800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr19:38470400-38470800	Enhancers	H1 Cell Line	embryonic stem cell
50	chr19:38470400-38470800	Enhancers	HUES64 Cell Line	embryonic stem cell

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