Variant report

Variant	rs12949039
Chromosome Location	chr17:17509721-17509722
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17504788..17507617-chr17:17507933..17511069,3	K562	blood:
2	chr17:17495233..17498168-chr17:17505537..17510752,5	MCF-7	breast:
3	chr17:17494037..17495633-chr17:17507321..17510221,2	K562	blood:
4	chr17:17397187..17399727-chr17:17509208..17511781,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133027	Chromatin interaction
ENSG00000108551	Chromatin interaction
ENSG00000264666	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11650499	0.91[ASN][1000 genomes]
rs11869600	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11871738	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12452584	0.85[ASN][1000 genomes]
rs12937108	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12937187	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939297	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12939598	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12941217	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12942708	0.89[ASN][1000 genomes]
rs12946063	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12946845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949336	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12950093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12951181	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952281	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952629	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34664666	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35372447	0.91[ASN][1000 genomes]
rs35660942	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35851484	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066210	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9911672	0.86[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	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17507000-17509800	Enhancers	K562	blood
2	chr17:17507000-17512600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:17507200-17510200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:17507200-17512600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:17507600-17509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:17508000-17510000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr17:17508000-17510400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:17508200-17510600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr17:17508400-17510600	Enhancers	Spleen	Spleen
10	chr17:17508400-17510800	Enhancers	NHDF-Ad	bronchial
11	chr17:17508600-17510200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:17508600-17510600	Enhancers	NHLF	lung
13	chr17:17508600-17515200	Weak transcription	Lung	lung
14	chr17:17508800-17509800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:17508800-17509800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr17:17508800-17510000	Enhancers	Hela-S3	cervix
17	chr17:17508800-17510200	Enhancers	Fetal Lung	lung
18	chr17:17509000-17509800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr17:17509200-17509800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:17509200-17509800	Enhancers	Fetal Intestine Small	intestine
21	chr17:17509200-17510000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:17509200-17510400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr17:17509200-17512600	Weak transcription	Right Ventricle	heart
24	chr17:17509400-17509800	Enhancers	Left Ventricle	heart
25	chr17:17509400-17515400	Weak transcription	HSMMtube	muscle
26	chr17:17509400-17517800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:17509600-17509800	Enhancers	Fetal Stomach	stomach
28	chr17:17509600-17510200	Enhancers	Fetal Heart	heart
29	chr17:17509600-17510200	Enhancers	Fetal Muscle Trunk	muscle
30	chr17:17509600-17510200	Enhancers	Right Atrium	heart
31	chr17:17509600-17510400	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links