Variant report

Variant	rs705492
Chromosome Location	chr19:38438538-38438539
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38434369..38435997-chr19:38437453..38439918,2	MCF-7	breast:
2	chr19:38395717..38398405-chr19:38438245..38443084,4	MCF-7	breast:
3	chr19:38423922..38426366-chr19:38436893..38438716,2	MCF-7	breast:
4	chr19:38396361..38399135-chr19:38437232..38439468,2	K562	blood:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10404567	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10415548	0.83[CEU][hapmap]
rs10420746	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1119229	0.88[CEU][hapmap]
rs12974225	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1643462	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1643463	0.95[EUR][1000 genomes]
rs1643466	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1643467	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1643468	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1643469	0.98[EUR][1000 genomes]
rs1725469	0.82[ASN][1000 genomes]
rs1725477	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1725478	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1725480	0.95[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs1725482	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs1725483	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725485	0.95[EUR][1000 genomes]
rs1725487	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725488	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1725494	0.97[EUR][1000 genomes]
rs1725499	0.83[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs241932	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2544718	0.97[EUR][1000 genomes]
rs35209753	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs353398	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353399	1.00[EUR][1000 genomes]
rs353400	1.00[EUR][1000 genomes]
rs353402	1.00[EUR][1000 genomes]
rs353403	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs353404	1.00[EUR][1000 genomes]
rs353407	1.00[EUR][1000 genomes]
rs353410	0.83[CEU][hapmap]
rs353411	0.83[CEU][hapmap]
rs353414	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353415	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs353416	1.00[EUR][1000 genomes]
rs353417	1.00[EUR][1000 genomes]
rs353419	1.00[EUR][1000 genomes]
rs353420	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353421	1.00[EUR][1000 genomes]
rs353423	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353424	1.00[EUR][1000 genomes]
rs353425	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353426	0.98[EUR][1000 genomes]
rs353427	1.00[EUR][1000 genomes]
rs353428	0.95[EUR][1000 genomes]
rs353429	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs353430	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3786869	0.83[CEU][hapmap]
rs4239516	0.83[CEU][hapmap]
rs4802135	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4803524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4803551	0.88[CEU][hapmap]
rs4803573	0.88[CEU][hapmap]
rs705491	0.88[CEU][hapmap]
rs705493	0.88[CEU][hapmap]
rs705494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs705495	0.88[CEU][hapmap]
rs705500	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7250409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7258597	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs752878	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8102579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8107341	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8112706	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs8113521	0.83[CEU][hapmap]
rs833895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs833896	0.94[EUR][1000 genomes]
rs833897	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs833898	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs833914	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs833926	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs856300	0.94[CEU][hapmap];0.81[CHB][hapmap]
rs856304	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs9304572	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][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	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
2	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs705492	WDR87	cis	Thyroid	GTEx
rs705492	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:38423200-38443000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:38423600-38444400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:38424600-38438800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:38424600-38439200	Weak transcription	Spleen	Spleen
6	chr19:38424800-38444000	Weak transcription	NHDF-Ad	bronchial
7	chr19:38425000-38441000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
9	chr19:38426400-38444000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr19:38426600-38442600	Weak transcription	HMEC	breast
11	chr19:38426600-38448200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:38426600-38450800	Weak transcription	Ovary	ovary
13	chr19:38426800-38439400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr19:38426800-38441000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr19:38426800-38443800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:38427000-38438600	Weak transcription	Brain Hippocampus Middle	brain
17	chr19:38427000-38438600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:38427000-38439400	Weak transcription	Lung	lung
19	chr19:38427000-38441000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:38427000-38441000	Weak transcription	Brain Germinal Matrix	brain
21	chr19:38427000-38441200	Weak transcription	Adipose Nuclei	Adipose
22	chr19:38427000-38441200	Weak transcription	Left Ventricle	heart
23	chr19:38427000-38444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:38427000-38444000	Weak transcription	Fetal Brain Female	brain
25	chr19:38427200-38443800	Weak transcription	NHEK	skin
26	chr19:38427200-38444200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:38427400-38443600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:38427600-38443600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:38428000-38441000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:38428600-38443400	Weak transcription	Fetal Stomach	stomach
31	chr19:38429200-38443800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:38429400-38441400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr19:38429800-38442600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:38430600-38444000	Weak transcription	HSMM	muscle
35	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
36	chr19:38432000-38440800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr19:38432400-38443200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr19:38432600-38439600	Weak transcription	NH-A	brain
39	chr19:38432600-38441200	Weak transcription	Esophagus	oesophagus
40	chr19:38432600-38442600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:38432600-38443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:38432800-38439600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:38432800-38443800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:38433000-38444000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:38433200-38439400	Genic enhancers	Fetal Intestine Small	intestine
46	chr19:38434000-38447800	Weak transcription	Hela-S3	cervix
47	chr19:38434200-38443000	Weak transcription	Right Atrium	heart
48	chr19:38434400-38438600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:38434400-38438600	Genic enhancers	A549	lung
50	chr19:38434400-38439200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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