Variant report

Variant	rs6587746
Chromosome Location	chr1:153485359-153485360
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153483559..153485959-chr1:153604351..153608068,3	MCF-7	breast:
2	chr1:153485153..153488099-chr1:153537854..153540911,4	K562	blood:
3	chr1:153363421..153365681-chr1:153484886..153487824,2	MCF-7	breast:
4	chr1:153474662..153477401-chr1:153483701..153485425,2	K562	blood:
5	chr1:153482943..153489100-chr1:153536653..153546582,24	MCF-7	breast:
6	chr1:153481535..153486377-chr1:153486910..153489741,6	MCF-7	breast:
7	chr1:153483402..153487706-chr1:153586614..153589553,6	MCF-7	breast:
8	chr1:153475901..153479398-chr1:153483925..153488105,4	K562	blood:
9	chr1:153480132..153490926-chr1:153537975..153544732,26	MCF-7	breast:
10	chr1:153482414..153491614-chr1:153504332..153509728,11	MCF-7	breast:
11	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
12	chr1:153482509..153486262-chr1:153580911..153583516,4	MCF-7	breast:
13	chr1:153485224..153486069-chr1:153540563..153541098,2	Hela-S3	cervix:
14	chr1:153484412..153486388-chr1:153498415..153500400,2	MCF-7	breast:
15	chr1:153483917..153485557-chr1:153585740..153588570,2	MCF-7	breast:
16	chr1:153485080..153486082-chr1:153540373..153541608,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000189171	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000163218	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000143546	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000188643	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs16835366	0.85[ASN][1000 genomes]
rs16835368	0.85[ASN][1000 genomes]
rs16835382	0.88[ASN][1000 genomes]
rs16835393	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17695220	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887039	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1964151	0.88[ASN][1000 genomes]
rs2094217	0.86[EUR][1000 genomes]
rs2094737	0.86[EUR][1000 genomes]
rs2094738	0.84[EUR][1000 genomes]
rs2262587	0.86[EUR][1000 genomes]
rs2339696	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480695	0.80[AMR][1000 genomes]
rs2480696	0.83[AMR][1000 genomes]
rs28410699	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28464843	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28632016	0.93[ASN][1000 genomes]
rs28635377	0.93[ASN][1000 genomes]
rs28676601	0.85[ASN][1000 genomes]
rs28707433	0.85[ASN][1000 genomes]
rs3915524	0.88[ASN][1000 genomes]
rs4272569	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4430277	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845351	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845352	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845548	0.85[ASN][1000 genomes]
rs4845549	0.88[ASN][1000 genomes]
rs4845550	0.88[ASN][1000 genomes]
rs4845551	0.88[ASN][1000 genomes]
rs4845552	0.93[ASN][1000 genomes]
rs4845553	0.93[ASN][1000 genomes]
rs4845554	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845555	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs532652	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs550597	0.80[AMR][1000 genomes]
rs6587743	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659755	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6660055	0.85[ASN][1000 genomes]
rs6679509	0.85[ASN][1000 genomes]
rs6684970	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6690638	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6690712	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696893	0.89[ASN][1000 genomes]
rs7515940	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7518306	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7520093	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534343	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534347	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534830	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537898	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544359	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9426945	0.86[EUR][1000 genomes]
rs9427239	0.86[EUR][1000 genomes]
rs9427287	0.86[EUR][1000 genomes]
rs9436094	0.85[ASN][1000 genomes]
rs9436095	0.93[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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153479200-153487600	Weak transcription	Small Intestine	intestine
2	chr1:153479800-153488000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:153480200-153488000	Weak transcription	Left Ventricle	heart
4	chr1:153480600-153485400	Weak transcription	Adipose Nuclei	Adipose
5	chr1:153480600-153485400	Weak transcription	Esophagus	oesophagus
6	chr1:153480600-153485400	Weak transcription	Right Atrium	heart
7	chr1:153480800-153487800	Weak transcription	Fetal Intestine Large	intestine
8	chr1:153481000-153488000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:153481000-153488000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:153481000-153488000	Weak transcription	Fetal Intestine Small	intestine
11	chr1:153481000-153490600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:153481200-153503600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:153481800-153486000	Enhancers	A549	lung
14	chr1:153482000-153485400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:153482200-153487600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:153482400-153488000	Weak transcription	Spleen	Spleen
17	chr1:153483200-153487000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr1:153483400-153485600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:153483400-153485800	Enhancers	HMEC	breast
20	chr1:153483400-153486000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:153483400-153486200	Enhancers	Hela-S3	cervix
22	chr1:153483600-153485400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:153483600-153485600	Enhancers	Stomach Mucosa	stomach
24	chr1:153483600-153487000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:153483600-153488800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:153483600-153493200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:153483800-153485400	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:153483800-153485400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:153483800-153486800	Weak transcription	Placenta	Placenta
30	chr1:153483800-153487800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:153483800-153487800	Weak transcription	Colonic Mucosa	Colon
32	chr1:153483800-153488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:153483800-153488000	Weak transcription	K562	blood
34	chr1:153483800-153497800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:153484000-153485400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:153484000-153485400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:153484000-153485400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:153484000-153487800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:153484000-153487800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:153484200-153485600	Weak transcription	Primary B cells from cord blood	blood
41	chr1:153484600-153486000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:153484800-153487800	Weak transcription	NHEK	skin
43	chr1:153485200-153485600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr1:153485200-153485800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:153485200-153486000	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:153485200-153488000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:153485200-153488000	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links