Variant report

Variant	rs2262587
Chromosome Location	chr1:153499485-153499486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153498468..153501057-chr1:153604609..153606478,2	MCF-7	breast:
2	chr1:153493804..153495495-chr1:153498906..153501485,2	K562	blood:
3	chr1:153483109..153485163-chr1:153497646..153499643,2	K562	blood:
4	chr1:153497935..153500148-chr1:153540288..153541980,2	MCF-7	breast:
5	chr1:153486911..153489748-chr1:153497891..153499485,2	MCF-7	breast:
6	chr1:153492181..153495094-chr1:153498850..153501392,2	MCF-7	breast:
7	chr1:153495315..153497702-chr1:153498619..153501151,2	MCF-7	breast:
8	chr1:153497091..153499956-chr1:153584552..153586138,2	MCF-7	breast:
9	chr1:153497834..153503028-chr1:153504169..153509062,7	MCF-7	breast:
10	chr1:153498168..153501408-chr1:153501922..153506252,5	K562	blood:
11	chr1:153498031..153500850-chr1:153536764..153538569,2	MCF-7	breast:
12	chr1:153498245..153501106-chr1:153506332..153508909,2	K562	blood:
13	chr1:153484412..153486388-chr1:153498415..153500400,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272030	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000197956	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs16835393	0.87[EUR][1000 genomes]
rs17695220	0.84[EUR][1000 genomes]
rs1887039	0.86[EUR][1000 genomes]
rs2094217	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094737	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094738	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248745	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2339696	0.84[EUR][1000 genomes]
rs2480695	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2480696	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28410699	0.86[EUR][1000 genomes]
rs28464843	0.84[EUR][1000 genomes]
rs28483109	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3762262	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4017737	0.82[ASN][1000 genomes]
rs4272569	0.94[EUR][1000 genomes]
rs4430277	0.94[EUR][1000 genomes]
rs477339	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845351	0.99[EUR][1000 genomes]
rs4845352	0.97[EUR][1000 genomes]
rs4845554	0.87[EUR][1000 genomes]
rs4845555	0.91[EUR][1000 genomes]
rs532652	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550597	0.84[EUR][1000 genomes]
rs552446	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs585215	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587743	0.84[EUR][1000 genomes]
rs6587745	0.86[EUR][1000 genomes]
rs6587746	0.86[EUR][1000 genomes]
rs659403	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6659755	0.93[EUR][1000 genomes]
rs6684970	0.96[EUR][1000 genomes]
rs6690638	0.86[EUR][1000 genomes]
rs6690712	0.86[EUR][1000 genomes]
rs7515940	0.86[EUR][1000 genomes]
rs7518306	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7520093	0.84[EUR][1000 genomes]
rs7534343	0.84[EUR][1000 genomes]
rs7534347	0.84[EUR][1000 genomes]
rs7534830	0.84[EUR][1000 genomes]
rs7537898	0.86[EUR][1000 genomes]
rs7544359	0.86[EUR][1000 genomes]
rs9426945	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427239	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427287	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153481200-153503600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:153489000-153506000	Weak transcription	Gastric	stomach
3	chr1:153493600-153504000	Weak transcription	Colonic Mucosa	Colon
4	chr1:153495600-153504800	Weak transcription	Spleen	Spleen
5	chr1:153496800-153500800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:153497200-153500400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:153497200-153500600	Enhancers	HMEC	breast
8	chr1:153497200-153504600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:153497400-153500800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:153497800-153499600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:153497800-153499600	Enhancers	Fetal Muscle Leg	muscle
12	chr1:153497800-153499800	Enhancers	HepG2	liver
13	chr1:153497800-153500000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:153497800-153500000	Enhancers	NHLF	lung
15	chr1:153497800-153500400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:153497800-153500400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr1:153497800-153500400	Enhancers	Fetal Heart	heart
18	chr1:153497800-153500600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:153498000-153499600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr1:153498000-153499600	Enhancers	Left Ventricle	heart
21	chr1:153498000-153500000	Enhancers	Placenta	Placenta
22	chr1:153498000-153500200	Enhancers	Esophagus	oesophagus
23	chr1:153498000-153500400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr1:153498000-153505800	Weak transcription	Aorta	Aorta
25	chr1:153498200-153499600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:153498200-153499600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:153498200-153499600	Flanking Active TSS	NHEK	skin
28	chr1:153498200-153499800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:153498200-153500200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:153498200-153505200	Weak transcription	Osteobl	bone
31	chr1:153498200-153506000	Weak transcription	Right Ventricle	heart
32	chr1:153498400-153499600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:153498400-153499600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:153498400-153499600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:153498400-153499800	Flanking Active TSS	K562	blood
36	chr1:153498400-153500000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:153498400-153500200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:153498400-153500600	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr1:153498400-153500800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:153498400-153500800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr1:153498400-153504600	Weak transcription	HSMM	muscle
42	chr1:153498400-153504600	Weak transcription	NHDF-Ad	bronchial
43	chr1:153498400-153504800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:153498400-153505400	Weak transcription	HSMMtube	muscle
45	chr1:153498600-153504600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:153498800-153499800	Weak transcription	Hela-S3	cervix
47	chr1:153498800-153505200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:153498800-153505200	Weak transcription	Right Atrium	heart
49	chr1:153499000-153499600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr1:153499000-153503600	Weak transcription	HUVEC	blood vessel

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