Variant report

Variant	rs28699609
Chromosome Location	chr18:43674879-43674880
allele	A/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	POLR2A	chr18:43674663-43675650	K562	blood:	n/a	n/a
2	SPI1	chr18:43674604-43674900	HL-60	blood:	n/a	chr18:43674702-43674715

No.	Distal block	Cell Line	Cell type
1	chr18:43666020..43671297-chr18:43672611..43675755,6	K562	blood:
2	chr18:43673300..43675362-chr18:43687086..43690045,2	MCF-7	breast:
3	chr18:43669796..43671297-chr18:43673823..43676678,2	K562	blood:
4	chr18:43673243..43676492-chr18:43676741..43681427,5	K562	blood:

Variant related genes	Relation type
ATP5A1	TF binding region
ENSG00000152234	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11082509	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11082510	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11659357	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11659478	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11659795	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11661945	0.91[EUR][1000 genomes]
rs11664764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11872954	0.93[EUR][1000 genomes]
rs11872985	0.93[EUR][1000 genomes]
rs11874712	0.94[EUR][1000 genomes]
rs12954944	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381709	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800637	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800639	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800640	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298787	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28457840	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28504655	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532950	0.85[EUR][1000 genomes]
rs28757346	0.85[EUR][1000 genomes]
rs34907121	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35507656	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3765636	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56075249	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56181324	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62096500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71364522	0.85[EUR][1000 genomes]
rs7230064	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7235373	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7244921	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244950	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8083998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8085444	0.91[EUR][1000 genomes]
rs8085743	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8088881	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8089150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091452	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8092674	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8093880	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8094902	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095031	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097521	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9304326	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9304327	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9304328	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9304330	0.83[EUR][1000 genomes]
rs9783884	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9783887	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9783888	0.91[EUR][1000 genomes]
rs9944637	0.91[EUR][1000 genomes]
rs9945606	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9945751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9947908	0.90[EUR][1000 genomes]
rs9954278	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9961065	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9962380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9962458	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43657200-43675000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr18:43657200-43675400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr18:43657200-43675400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr18:43657200-43675600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr18:43657200-43676000	Strong transcription	Osteobl	bone
6	chr18:43657200-43676200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr18:43657400-43675000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr18:43657400-43675200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr18:43657400-43675400	Strong transcription	Placenta	Placenta
10	chr18:43657400-43675800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr18:43657400-43675800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr18:43657600-43675200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr18:43657800-43675200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr18:43657800-43675800	Strong transcription	Fetal Muscle Leg	muscle
15	chr18:43657800-43676600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr18:43658000-43675400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr18:43658600-43675000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr18:43658600-43675400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr18:43659000-43675200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr18:43659000-43675200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr18:43659000-43676000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr18:43659200-43675000	Strong transcription	Fetal Brain Female	brain
23	chr18:43659200-43675800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr18:43659400-43675800	Strong transcription	HMEC	breast
25	chr18:43660600-43675200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr18:43660600-43675400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr18:43661200-43675400	Strong transcription	NHEK	skin
28	chr18:43663000-43675200	Strong transcription	NHDF-Ad	bronchial
29	chr18:43663400-43675400	Strong transcription	NH-A	brain
30	chr18:43665200-43675600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr18:43669400-43675600	Strong transcription	K562	blood
32	chr18:43669600-43676200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr18:43669800-43675200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr18:43669800-43675800	Strong transcription	Fetal Intestine Large	intestine
35	chr18:43669800-43676000	Strong transcription	Fetal Thymus	thymus
36	chr18:43670000-43675400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr18:43670000-43676000	Weak transcription	Aorta	Aorta
38	chr18:43670000-43676400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr18:43670000-43676600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr18:43670200-43675400	Weak transcription	Right Ventricle	heart
41	chr18:43670200-43675400	Weak transcription	Small Intestine	intestine
42	chr18:43670400-43677200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr18:43670600-43676800	Weak transcription	Stomach Mucosa	stomach
44	chr18:43670800-43675800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr18:43671600-43675600	Strong transcription	Fetal Stomach	stomach
46	chr18:43671600-43676200	Strong transcription	Fetal Intestine Small	intestine
47	chr18:43671800-43675600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr18:43671800-43675800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:43671800-43676000	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr18:43671800-43676600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links