Variant report

Variant	rs16998499
Chromosome Location	chr20:52492634-52492635
allele	A/G
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	TEAD4	chr20:52491841-52492761	A549	lung:	n/a	n/a
2	GATA3	chr20:52485403-52492846	MCF-7	breast:	n/a	chr20:52491283-52491293 chr20:52488794-52488803 chr20:52488939-52488949 chr20:52490093-52490103 chr20:52492097-52492106 chr20:52491504-52491520 chr20:52491284-52491291 chr20:52491284-52491293
3	POLR2A	chr20:52491850-52492715	HL-60	blood:	n/a	n/a
4	GABPA	chr20:52491963-52492639	HL-60	blood:	n/a	n/a
5	GABPA	chr20:52491780-52492717	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:52476331..52478777-chr20:52492357..52493924,2	K562	blood:
2	chr20:52490662..52493657-chr3:155587949..155590436,2	MCF-7	breast:
3	chr1:144930770..144933506-chr20:52490207..52493077,2	MCF-7	breast:
4	chr17:57920677..57923064-chr20:52492211..52494157,2	MCF-7	breast:
5	chr20:50382823..50385492-chr20:52491964..52494006,2	MCF-7	breast:

Variant related genes	Relation type
SUMO1P1	TF binding region
ENSG00000178104	Chromatin interaction
ENSG00000163655	Chromatin interaction
ENSG00000054793	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16998502	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16998533	1.00[EUR][1000 genomes]
rs16998893	1.00[MEX][hapmap]
rs57886257	1.00[EUR][1000 genomes]
rs58979406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59046998	1.00[EUR][1000 genomes]
rs6022721	1.00[AMR][1000 genomes]
rs7262342	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73275816	1.00[EUR][1000 genomes]
rs73275820	1.00[EUR][1000 genomes]
rs73914417	1.00[EUR][1000 genomes]
rs73914419	1.00[EUR][1000 genomes]
rs73914429	1.00[EUR][1000 genomes]
rs73914430	1.00[EUR][1000 genomes]
rs73914434	1.00[EUR][1000 genomes]
rs8114189	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
6	nsv586222	chr20:52473679-52506380	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	74 gene(s)	inside rSNPs	diseases
7	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52483400-52495000	Weak transcription	Spleen	Spleen
2	chr20:52485000-52493000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:52487400-52495000	Weak transcription	Small Intestine	intestine
4	chr20:52487400-52495400	Weak transcription	K562	blood
5	chr20:52489000-52493200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr20:52489000-52494600	Weak transcription	Liver	Liver
7	chr20:52490000-52494000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr20:52490000-52494400	Weak transcription	Fetal Kidney	kidney
9	chr20:52490000-52494800	Weak transcription	A549	lung
10	chr20:52490000-52495000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr20:52490200-52493200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr20:52490200-52493800	Weak transcription	HepG2	liver
13	chr20:52490200-52494800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr20:52490200-52494800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr20:52490200-52495000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr20:52490200-52495200	Weak transcription	Fetal Lung	lung
17	chr20:52490200-52495400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr20:52490200-52495400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr20:52490200-52495400	Weak transcription	Fetal Muscle Leg	muscle
20	chr20:52490200-52496600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr20:52490200-52499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr20:52490200-52501200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr20:52490200-52502400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr20:52490400-52493200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr20:52490400-52493400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr20:52490400-52494600	Weak transcription	Fetal Intestine Small	intestine
27	chr20:52490400-52495000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr20:52490400-52495400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr20:52490400-52495600	Weak transcription	Fetal Thymus	thymus
30	chr20:52490600-52495400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr20:52490600-52497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr20:52491000-52494800	Weak transcription	Fetal Intestine Large	intestine
33	chr20:52491000-52495000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr20:52491000-52495600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr20:52491200-52492800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr20:52492000-52493400	Enhancers	Gastric	stomach
37	chr20:52492200-52493400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr20:52492600-52493000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr20:52492600-52493200	Weak transcription	Brain Germinal Matrix	brain
40	chr20:52492600-52495600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr20:52492600-52496600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr20:52492600-52501200	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links