Variant report

Variant	rs705491
Chromosome Location	chr19:38438694-38438695
allele	A/G
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	chr19:38438618..38442193-chr19:38444314..38446890,3	MCF-7	breast:
3	chr19:38395717..38398405-chr19:38438245..38443084,4	MCF-7	breast:
4	chr19:38423922..38426366-chr19:38436893..38438716,2	MCF-7	breast:
5	chr19:38396361..38399135-chr19:38437232..38439468,2	K562	blood:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10404159	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10404567	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs10415399	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10420746	0.88[CEU][hapmap]
rs11083441	0.91[EUR][1000 genomes]
rs1119229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap]
rs12608883	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12973580	0.90[EUR][1000 genomes]
rs12974225	0.88[CEU][hapmap]
rs1643460	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1643461	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1643466	0.87[CEU][hapmap]
rs1643467	0.87[CEU][hapmap]
rs1643468	0.87[CEU][hapmap]
rs1725481	0.88[CEU][hapmap]
rs1725482	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs1725499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075281	0.88[CEU][hapmap]
rs241932	0.88[CEU][hapmap]
rs28460297	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs353410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353411	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353414	0.87[CEU][hapmap]
rs353415	0.88[CEU][hapmap]
rs353423	0.87[CEU][hapmap]
rs3786869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3865514	1.00[YRI][hapmap]
rs4239516	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4802144	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4802147	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4802151	0.83[EUR][1000 genomes]
rs4803524	0.88[CEU][hapmap]
rs4803551	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705492	0.88[CEU][hapmap]
rs705493	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[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705494	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705499	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250409	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs8102579	0.88[CEU][hapmap]
rs8108434	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109053	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109835	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8110284	0.87[CEU][hapmap]
rs8112706	0.87[CEU][hapmap]
rs8113273	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8113521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs833895	0.87[CEU][hapmap]
rs833926	0.88[CEU][hapmap]
rs856300	0.82[CEU][hapmap]
rs856304	0.88[CEU][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs705491	CBLC	cis	parietal	SCAN
rs705491	PHLDB3	cis	parietal	SCAN
rs705491	PAFAH1B3	cis	cerebellum	SCAN
rs705491	PHLDB3	cis	cerebellum	SCAN
rs705491	HIF3A	cis	parietal	SCAN
rs705491	DMPK	cis	parietal	SCAN
rs705491	AC012309.5	cis	Artery Tibial	GTEx

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	chr19:38427000-38439400	Weak transcription	Lung	lung
17	chr19:38427000-38441000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:38427000-38441000	Weak transcription	Brain Germinal Matrix	brain
19	chr19:38427000-38441200	Weak transcription	Adipose Nuclei	Adipose
20	chr19:38427000-38441200	Weak transcription	Left Ventricle	heart
21	chr19:38427000-38444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:38427000-38444000	Weak transcription	Fetal Brain Female	brain
23	chr19:38427200-38443800	Weak transcription	NHEK	skin
24	chr19:38427200-38444200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:38427400-38443600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:38427600-38443600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:38428000-38441000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:38428600-38443400	Weak transcription	Fetal Stomach	stomach
29	chr19:38429200-38443800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr19:38429400-38441400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr19:38429800-38442600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr19:38430600-38444000	Weak transcription	HSMM	muscle
33	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
34	chr19:38432000-38440800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:38432400-38443200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr19:38432600-38439600	Weak transcription	NH-A	brain
37	chr19:38432600-38441200	Weak transcription	Esophagus	oesophagus
38	chr19:38432600-38442600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:38432600-38443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:38432800-38439600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:38432800-38443800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:38433000-38444000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:38433200-38439400	Genic enhancers	Fetal Intestine Small	intestine
44	chr19:38434000-38447800	Weak transcription	Hela-S3	cervix
45	chr19:38434200-38443000	Weak transcription	Right Atrium	heart
46	chr19:38434400-38439200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:38434400-38439200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:38434400-38439200	Weak transcription	Osteobl	bone
49	chr19:38434400-38440800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:38434400-38441000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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