Variant report

Variant	rs6539708
Chromosome Location	chr12:83593119-83593120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:83592254..83594970-chr12:83596258..83598590,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10746271	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10778949	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10862604	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10862605	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11115641	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1356441	0.82[EUR][1000 genomes]
rs1356442	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1517814	0.83[EUR][1000 genomes]
rs2037258	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2037259	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2037260	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2403091	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2403092	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2403093	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2896455	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4242871	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4882555	0.84[EUR][1000 genomes]
rs4882556	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4882557	0.83[EUR][1000 genomes]
rs6539709	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6539711	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6539713	0.86[EUR][1000 genomes]
rs71445206	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7301011	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7302888	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7316717	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7953127	0.87[EUR][1000 genomes]
rs7962167	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7962962	0.87[EUR][1000 genomes]
rs7964401	0.86[AMR][1000 genomes]
rs7973484	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7979811	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs970483	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv559559	chr12:83505512-83765069	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv899352	chr12:83556258-83671428	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83590600-83594600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:83591800-83594000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr12:83592000-83593200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:83592000-83593200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:83592000-83593200	Enhancers	Colon Smooth Muscle	Colon
6	chr12:83592000-83594000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr12:83592200-83593200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:83592200-83593200	Active TSS	Brain Anterior Caudate	brain
9	chr12:83592200-83593200	Enhancers	Fetal Lung	lung
10	chr12:83592200-83593800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr12:83592400-83593200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr12:83592400-83593200	Active TSS	Brain Hippocampus Middle	brain
13	chr12:83592400-83593200	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr12:83592400-83593200	Enhancers	Fetal Kidney	kidney
15	chr12:83592800-83593200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:83592800-83593200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:83592800-83593200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:83592800-83595400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:83593000-83593400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr12:83593000-83593800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr12:83593000-83594000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr12:83593000-83594400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr12:83593000-83597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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