Variant report

Variant	rs62137816
Chromosome Location	chr19:19713353-19713354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr19:19712932-19713434	MCF-7	breast:	n/a	n/a
2	GATA3	chr19:19712871-19713442	MCF-7	breast:	n/a	n/a
3	E2F4	chr19:19713226-19713397	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr19:19712885-19714021	MCF10A-Er-Src	breast:	n/a	n/a
5	TCF7L2	chr19:19712915-19713503	MCF-7	breast:	n/a	chr19:19713206-19713220 chr19:19713184-19713198

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19626874..19628418-chr19:19712468..19714125,2	K562	blood:

Variant related genes	Relation type
ENSG00000259242	TF binding region
ENSG00000258674	Chromatin interaction
ENSG00000186010	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12611058	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974028	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12977917	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12981270	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12982628	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12985142	0.90[EUR][1000 genomes]
rs1476459	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33982830	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34096655	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34316070	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34316527	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34324119	0.92[EUR][1000 genomes]
rs34424437	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35209041	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35437712	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35553578	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35842591	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56083851	0.92[EUR][1000 genomes]
rs62134460	0.92[EUR][1000 genomes]
rs62137783	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137820	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62137822	0.93[EUR][1000 genomes]
rs7247165	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73004920	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs750216	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv518076	chr19:19692579-19715794	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19702600-19713400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:19702600-19713400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr19:19702600-19713600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr19:19702600-19719400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:19703400-19717000	Weak transcription	Fetal Muscle Leg	muscle
6	chr19:19703800-19717000	Weak transcription	Spleen	Spleen
7	chr19:19706600-19713600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr19:19706600-19717000	Weak transcription	Esophagus	oesophagus
9	chr19:19706600-19728200	Weak transcription	Fetal Brain Male	brain
10	chr19:19707000-19718600	Weak transcription	Fetal Lung	lung
11	chr19:19707200-19717000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr19:19707400-19716800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:19707600-19716800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:19707600-19728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:19707800-19714000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:19707800-19716800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:19708000-19716800	Enhancers	Fetal Thymus	thymus
18	chr19:19708800-19715000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:19708800-19716800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr19:19708800-19720000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:19708800-19724400	Weak transcription	NHDF-Ad	bronchial
22	chr19:19709000-19713600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:19709000-19719200	Weak transcription	Fetal Brain Female	brain
24	chr19:19710200-19714600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr19:19710200-19716800	Weak transcription	Dnd41	blood
26	chr19:19710200-19718800	Weak transcription	Fetal Stomach	stomach
27	chr19:19710400-19713400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr19:19711600-19714600	Enhancers	Thymus	Thymus
29	chr19:19711800-19714200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr19:19712000-19713600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr19:19712000-19714000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:19712000-19714000	Enhancers	GM12878-XiMat	blood
33	chr19:19712000-19714600	Enhancers	Stomach Mucosa	stomach
34	chr19:19712200-19713800	Enhancers	Brain Germinal Matrix	brain
35	chr19:19712600-19713400	Enhancers	Placenta	Placenta
36	chr19:19712600-19714000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:19712600-19714200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr19:19712600-19714200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr19:19712600-19714400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:19712800-19713400	Enhancers	HepG2	liver
41	chr19:19712800-19713600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:19712800-19713600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:19712800-19713800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:19712800-19714600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:19712800-19719400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:19712800-19724400	Weak transcription	Gastric	stomach
47	chr19:19713000-19713400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr19:19713000-19713400	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr19:19713000-19713400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr19:19713000-19713400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links