Variant report

Variant	rs705499
Chromosome Location	chr19:38440494-38440495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38438618..38442193-chr19:38444314..38446890,3	MCF-7	breast:
2	chr19:38395717..38398405-chr19:38438245..38443084,4	MCF-7	breast:
3	chr19:38440256..38441798-chr19:38479359..38480943,2	K562	blood:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10404159	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10415399	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415548	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083441	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12608883	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12973580	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1643460	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1643461	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1725499	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28460297	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs353410	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353411	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3786869	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4239516	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4802144	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4802147	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4802151	0.81[EUR][1000 genomes]
rs4803551	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803573	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705491	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705493	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705495	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8108434	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109053	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109835	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8113273	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8113521	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[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

No data

Chromatin state (count:76 , 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	chr19:38424800-38444000	Weak transcription	NHDF-Ad	bronchial
5	chr19:38425000-38441000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
7	chr19:38426400-38444000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:38426600-38442600	Weak transcription	HMEC	breast
9	chr19:38426600-38448200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:38426600-38450800	Weak transcription	Ovary	ovary
11	chr19:38426800-38441000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr19:38426800-38443800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr19:38427000-38441000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:38427000-38441000	Weak transcription	Brain Germinal Matrix	brain
15	chr19:38427000-38441200	Weak transcription	Adipose Nuclei	Adipose
16	chr19:38427000-38441200	Weak transcription	Left Ventricle	heart
17	chr19:38427000-38444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:38427000-38444000	Weak transcription	Fetal Brain Female	brain
19	chr19:38427200-38443800	Weak transcription	NHEK	skin
20	chr19:38427200-38444200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:38427400-38443600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:38427600-38443600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:38428000-38441000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:38428600-38443400	Weak transcription	Fetal Stomach	stomach
25	chr19:38429200-38443800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr19:38429400-38441400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr19:38429800-38442600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:38430600-38444000	Weak transcription	HSMM	muscle
29	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
30	chr19:38432000-38440800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:38432400-38443200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr19:38432600-38441200	Weak transcription	Esophagus	oesophagus
33	chr19:38432600-38442600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:38432600-38443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:38432800-38443800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:38433000-38444000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:38434000-38447800	Weak transcription	Hela-S3	cervix
38	chr19:38434200-38443000	Weak transcription	Right Atrium	heart
39	chr19:38434400-38440800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:38434400-38441000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:38434400-38441200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:38434400-38444200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:38434400-38451800	Weak transcription	Primary T cells from cord blood	blood
44	chr19:38435200-38444000	Weak transcription	Colonic Mucosa	Colon
45	chr19:38436600-38443800	Weak transcription	Fetal Intestine Large	intestine
46	chr19:38436600-38444000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr19:38437200-38441800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr19:38438400-38455600	Enhancers	Primary B cells from peripheral blood	blood
49	chr19:38438600-38441800	Genic enhancers	GM12878-XiMat	blood
50	chr19:38438800-38441000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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