Variant report

Variant	rs13061948
Chromosome Location	chr3:28546773-28546774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10460986	0.87[ASN][1000 genomes]
rs11717248	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11717630	0.81[ASN][1000 genomes]
rs12054331	0.82[CHB][hapmap]
rs13064600	0.86[ASN][1000 genomes]
rs13070954	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs1379656	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs1457908	0.83[ASN][1000 genomes]
rs1563656	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1585211	0.81[AFR][1000 genomes]
rs1598845	0.81[ASN][1000 genomes]
rs1982560	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs34741404	0.83[ASN][1000 genomes]
rs4339073	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4637245	0.81[ASN][1000 genomes]
rs4680915	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs4680916	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6549859	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6551253	0.83[CEU][hapmap]
rs6777813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7427045	0.82[ASN][1000 genomes]
rs7612033	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs7633162	0.81[CHB][hapmap]
rs974933	0.87[CHB][hapmap]
rs9854180	0.87[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv876650	chr3:28427029-28613602	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1015015	chr3:28461972-28728494	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv916364	chr3:28468275-29146280	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv590010	chr3:28469830-28727214	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1004457	chr3:28541307-28595311	Strong transcription Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28514800-28575800	Weak transcription	Ovary	ovary
2	chr3:28544400-28549400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:28546000-28547200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr3:28546000-28548000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:28546200-28546800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:28546200-28547200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:28546200-28547200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:28546200-28547400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:28546200-28547400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:28546200-28548000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:28546400-28547000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:28546400-28547400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:28546400-28548000	Enhancers	Brain Germinal Matrix	brain
14	chr3:28546600-28546800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:28546600-28546800	Enhancers	Psoas Muscle	Psoas
16	chr3:28546600-28547200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:28546600-28547200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:28546600-28547200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:28546600-28547200	Enhancers	Fetal Heart	heart
20	chr3:28546600-28548400	Enhancers	Cortex derived primary cultured neurospheres	brain

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