Variant report

Variant	rs62112289
Chromosome Location	chr19:38430755-38430756
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38426351..38429541-chr19:38429679..38432396,3	MCF-7	breast:
2	chr19:38429570..38433364-chr19:38470420..38473384,4	MCF-7	breast:
3	chr19:38429620..38432049-chr19:38435086..38437572,3	K562	blood:
4	chr19:38395644..38401186-chr19:38430482..38434552,8	MCF-7	breast:
5	chr19:38421583..38424887-chr19:38429672..38432254,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs62110229	0.81[ASN][1000 genomes]
rs62110230	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62110232	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62112272	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112273	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112274	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62112275	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112277	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112279	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62112280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112285	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112286	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112288	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62120128	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62120129	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62120130	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62120131	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7257838	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258680	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8105754	0.80[EUR][1000 genomes];0.81[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:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:38423000-38438200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:38423200-38443000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:38423400-38433800	Weak transcription	Thymus	Thymus
6	chr19:38423600-38444400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:38424600-38438800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:38424600-38439200	Weak transcription	Spleen	Spleen
9	chr19:38424800-38444000	Weak transcription	NHDF-Ad	bronchial
10	chr19:38425000-38431200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:38425000-38431600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:38425000-38432200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:38425000-38438400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr19:38425000-38441000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
16	chr19:38425200-38436000	Enhancers	Stomach Mucosa	stomach
17	chr19:38426400-38432200	Weak transcription	NH-A	brain
18	chr19:38426400-38435600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr19:38426400-38444000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:38426600-38435000	Weak transcription	HUVEC	blood vessel
21	chr19:38426600-38438200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:38426600-38442600	Weak transcription	HMEC	breast
23	chr19:38426600-38448200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:38426600-38450800	Weak transcription	Ovary	ovary
25	chr19:38426800-38431800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr19:38426800-38438400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:38426800-38439400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr19:38426800-38441000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr19:38426800-38443800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:38427000-38431200	Weak transcription	Gastric	stomach
31	chr19:38427000-38433800	Weak transcription	Right Atrium	heart
32	chr19:38427000-38438600	Weak transcription	Brain Hippocampus Middle	brain
33	chr19:38427000-38438600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:38427000-38439400	Weak transcription	Lung	lung
35	chr19:38427000-38441000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:38427000-38441000	Weak transcription	Brain Germinal Matrix	brain
37	chr19:38427000-38441200	Weak transcription	Adipose Nuclei	Adipose
38	chr19:38427000-38441200	Weak transcription	Left Ventricle	heart
39	chr19:38427000-38444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:38427000-38444000	Weak transcription	Fetal Brain Female	brain
41	chr19:38427200-38433800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:38427200-38438400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:38427200-38443800	Weak transcription	NHEK	skin
44	chr19:38427200-38444200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:38427400-38431400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr19:38427400-38431600	Weak transcription	Pancreas	Pancrea
47	chr19:38427400-38432200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:38427400-38432200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:38427400-38432200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:38427400-38443600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links