Variant report

Variant	rs13039601
Chromosome Location	chr20:52841034-52841035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52840058..52843007-chr20:53284448..53286480,2	MCF-7	breast:
2	chr20:52839394..52842266-chr3:64681661..64683712,2	MCF-7	breast:
3	chr20:52840503..52842605-chr6:20208710..20211532,2	MCF-7	breast:
4	chr20:52840265..52842144-chr20:52866787..52869345,2	MCF-7	breast:
5	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
6	chr20:52838493..52841252-chr20:52870452..52872363,2	MCF-7	breast:
7	chr20:52838614..52841427-chr20:52933611..52935858,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13039589	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13042527	0.97[EUR][1000 genomes]
rs13045276	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13045683	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1477725	0.93[EUR][1000 genomes]
rs16999299	0.82[TSI][hapmap]
rs17223034	0.83[CEU][hapmap];0.89[MEX][hapmap]
rs1964861	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2023531	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs28404865	0.91[EUR][1000 genomes]
rs28435070	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28526259	0.85[EUR][1000 genomes]
rs28676447	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28707344	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6013946	0.81[EUR][1000 genomes]
rs6023080	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs6023083	0.88[CEU][hapmap];0.81[EUR][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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13039601	DOK5	cis	parietal	SCAN
rs13039601	PFDN4	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52829400-52847400	Weak transcription	Aorta	Aorta
2	chr20:52829600-52847600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr20:52831400-52842200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr20:52833000-52845400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:52834200-52841200	Weak transcription	Spleen	Spleen
6	chr20:52834200-52843600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr20:52834600-52843600	Weak transcription	GM12878-XiMat	blood
8	chr20:52834600-52845200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:52834600-52845200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr20:52834600-52845200	Weak transcription	NHEK	skin
11	chr20:52835600-52845800	Weak transcription	HSMM	muscle
12	chr20:52835600-52846000	Weak transcription	HSMMtube	muscle
13	chr20:52837400-52842200	Weak transcription	Dnd41	blood
14	chr20:52838600-52846000	Weak transcription	Fetal Muscle Leg	muscle
15	chr20:52839200-52842200	Weak transcription	HepG2	liver
16	chr20:52839200-52843800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr20:52839400-52841600	Weak transcription	Fetal Stomach	stomach
18	chr20:52839600-52845400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr20:52840000-52841200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr20:52840600-52849000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr20:52840800-52849000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr20:52841000-52851000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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