Variant report

Variant	rs9845406
Chromosome Location	chr3:134888541-134888542
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10804635	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1159404	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs11712935	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12636613	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12636659	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13063564	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13076510	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs13087756	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1392918	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1404577	0.85[JPT][hapmap]
rs1501205	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1501206	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1501207	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1501219	0.93[YRI][hapmap]
rs2270882	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291989	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3772638	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772640	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3772647	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3772648	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3821503	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7372088	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7373413	0.85[JPT][hapmap]
rs7620133	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642038	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9883173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv877516	chr3:134689420-134918522	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134874800-134901800	Weak transcription	GM12878-XiMat	blood
2	chr3:134879000-134889600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:134880800-134889400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:134880800-134889600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:134880800-134889800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:134881200-134891000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:134885000-134904400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:134885600-134911800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:134885600-134912200	Weak transcription	Brain Germinal Matrix	brain
10	chr3:134885800-134892000	Weak transcription	Brain Substantia Nigra	brain
11	chr3:134886200-134890200	Weak transcription	Fetal Brain Male	brain
12	chr3:134887000-134888800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:134887000-134890600	Enhancers	Liver	Liver
14	chr3:134887200-134888600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:134887200-134889400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:134887600-134911400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:134888000-134889000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:134888000-134889600	Weak transcription	Psoas Muscle	Psoas
19	chr3:134888000-134891200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:134888200-134888600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:134888200-134900000	Weak transcription	Fetal Brain Female	brain
22	chr3:134888200-134908600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:134888400-134889000	Enhancers	Brain Anterior Caudate	brain
24	chr3:134888400-134889800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:134888400-134890000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:134888400-134891000	Enhancers	HUES64 Cell Line	embryonic stem cell

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