Variant report

Variant	rs6782004
Chromosome Location	chr3:134684918-134684919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11707505	1.00[JPT][hapmap]
rs11707539	1.00[JPT][hapmap]
rs11719020	1.00[JPT][hapmap]
rs12495634	1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs1457560	1.00[JPT][hapmap]
rs1457562	1.00[JPT][hapmap]
rs1457563	1.00[JPT][hapmap]
rs1562508	1.00[JPT][hapmap]
rs1562509	1.00[JPT][hapmap]
rs185257	1.00[JPT][hapmap]
rs1870196	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs1982548	1.00[JPT][hapmap]
rs2045451	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3772657	0.81[CEU][hapmap]
rs3940695	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955459	1.00[JPT][hapmap]
rs4955460	0.80[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955461	0.85[JPT][hapmap]
rs4955462	0.81[AMR][1000 genomes]
rs4955520	1.00[JPT][hapmap]
rs4955522	1.00[JPT][hapmap]
rs4955524	1.00[JPT][hapmap]
rs4955527	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4955531	0.81[AMR][1000 genomes]
rs6439537	1.00[JPT][hapmap]
rs6439538	1.00[JPT][hapmap]
rs6768729	1.00[JPT][hapmap]
rs6769854	0.84[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6776308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781640	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs6789372	0.90[CEU][hapmap];0.80[MEX][hapmap]
rs6795875	1.00[JPT][hapmap]
rs6799875	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6806959	1.00[JPT][hapmap]
rs7636504	0.84[CHD][hapmap];0.84[TSI][hapmap]
rs7644369	1.00[JPT][hapmap]
rs9289487	1.00[JPT][hapmap]
rs936323	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs936324	1.00[JPT][hapmap]
rs936325	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs972234	1.00[JPT][hapmap]
rs975148	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9815290	1.00[JPT][hapmap]
rs9818859	0.80[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9825380	1.00[JPT][hapmap]
rs9856814	1.00[JPT][hapmap]
rs9859282	1.00[JPT][hapmap]
rs9868665	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9869233	1.00[JPT][hapmap]
rs9874260	0.80[ASW][hapmap];0.91[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[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	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
2	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
3	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:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134671000-134693400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:134671000-134697400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:134677400-134697400	Weak transcription	GM12878-XiMat	blood
4	chr3:134677800-134697000	Weak transcription	Psoas Muscle	Psoas
5	chr3:134678600-134699400	Weak transcription	Aorta	Aorta
6	chr3:134680200-134692800	Weak transcription	Spleen	Spleen
7	chr3:134683000-134690200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:134684000-134685800	Enhancers	Fetal Brain Male	brain
9	chr3:134684200-134685800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:134684400-134685800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:134684400-134685800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:134684600-134685200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:134684600-134685200	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr3:134684600-134685400	Enhancers	Brain Substantia Nigra	brain
15	chr3:134684600-134685600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:134684600-134685600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr3:134684600-134685600	Enhancers	Brain Anterior Caudate	brain
18	chr3:134684600-134685800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:134684600-134685800	Enhancers	Brain Cingulate Gyrus	brain
20	chr3:134684600-134685800	Enhancers	Fetal Brain Female	brain
21	chr3:134684600-134686000	Enhancers	Brain Germinal Matrix	brain
22	chr3:134684800-134685400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:134684800-134686000	Enhancers	Brain Hippocampus Middle	brain

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