Variant report

Variant	rs3909402
Chromosome Location	chr5:167431268-167431269
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:167426744..167429532-chr5:167429967..167431982,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10042104	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10052830	0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10064267	1.00[EUR][1000 genomes]
rs10065915	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10076491	0.82[EUR][1000 genomes]
rs10475863	1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11953311	1.00[CEU][hapmap]
rs11954345	1.00[CEU][hapmap]
rs13359764	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs17069337	1.00[CEU][hapmap]
rs17069538	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17069541	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17069614	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs17069629	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs2011893	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2019072	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs3909403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909404	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869080	1.00[CEU][hapmap]
rs73803833	0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830546	chr5:167303135-167456271	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167413800-167432000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:167423400-167440600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:167423400-167455400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:167423800-167432000	Weak transcription	HMEC	breast
5	chr5:167427000-167434400	Weak transcription	Left Ventricle	heart
6	chr5:167428200-167432800	Weak transcription	Brain Angular Gyrus	brain
7	chr5:167428400-167432400	Weak transcription	Right Ventricle	heart
8	chr5:167428400-167433200	Weak transcription	HSMM	muscle
9	chr5:167428600-167433200	Weak transcription	Ovary	ovary
10	chr5:167429000-167437600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:167429400-167433000	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:167429400-167433200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:167429600-167432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:167430000-167432200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:167430200-167431800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:167430800-167433000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:167431000-167432600	Enhancers	NHEK	skin
18	chr5:167431200-167432600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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