Variant report

Variant	rs6439529
Chromosome Location	chr3:134583376-134583377
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11706968	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs11928990	0.89[CHB][hapmap]
rs12489463	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs12496060	0.88[CHB][hapmap]
rs13068347	0.92[JPT][hapmap]
rs13072597	0.86[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs13072762	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13073658	0.89[CHB][hapmap]
rs13078595	0.84[JPT][hapmap]
rs13079457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13090529	0.89[CHB][hapmap]
rs13090749	0.89[CHB][hapmap]
rs13090758	0.89[CHB][hapmap]
rs13091440	0.89[CHB][hapmap]
rs1399707	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1399710	0.82[JPT][hapmap]
rs1515367	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1949305	0.89[CHB][hapmap]
rs2280156	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292659	0.89[CHB][hapmap]
rs2292660	0.89[CHB][hapmap]
rs34287501	0.82[EUR][1000 genomes]
rs34640730	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35287767	0.80[ASN][1000 genomes]
rs3732569	0.89[CHB][hapmap]
rs60531499	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439530	0.92[JPT][hapmap]
rs6762261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6762621	0.83[JPT][hapmap]
rs6782516	0.89[CHB][hapmap]
rs6785725	0.82[EUR][1000 genomes]
rs6789763	0.90[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs6793813	0.86[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs6797353	0.82[EUR][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	nsv877515	chr3:134460368-134591138	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134580800-134586200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:134581400-134583400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:134581600-134583400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:134582200-134583800	Enhancers	Fetal Brain Female	brain
5	chr3:134582200-134584000	Enhancers	Fetal Brain Male	brain
6	chr3:134582600-134583400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:134582600-134583400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr3:134582600-134584200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:134582800-134583400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:134582800-134583400	Enhancers	H9 Cell Line	embryonic stem cell
11	chr3:134582800-134583400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:134582800-134583400	Enhancers	Right Atrium	heart
13	chr3:134582800-134583400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:134582800-134583600	Enhancers	Rectal Smooth Muscle	rectum
15	chr3:134582800-134583800	Enhancers	Brain Germinal Matrix	brain
16	chr3:134583000-134583400	Enhancers	Right Ventricle	heart
17	chr3:134583000-134583400	Enhancers	GM12878-XiMat	blood
18	chr3:134583000-134583600	Bivalent Enhancer	HUVEC	blood vessel
19	chr3:134583000-134583800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:134583000-134583800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:134583000-134583800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr3:134583000-134583800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:134583000-134583800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:134583000-134583800	Enhancers	Adipose Nuclei	Adipose
25	chr3:134583000-134583800	Enhancers	Fetal Muscle Leg	muscle
26	chr3:134583000-134583800	Enhancers	Fetal Stomach	stomach
27	chr3:134583000-134583800	Enhancers	Left Ventricle	heart
28	chr3:134583000-134584000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:134583200-134583400	Enhancers	Fetal Lung	lung
30	chr3:134583200-134583600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr3:134583200-134583800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:134583200-134583800	Enhancers	Spleen	Spleen
33	chr3:134583200-134583800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr3:134583200-134587600	Weak transcription	Psoas Muscle	Psoas

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