Variant report

Variant	rs2039987
Chromosome Location	chr6:142655490-142655491
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142648503..142651872-chr6:142652500..142656138,3	MCF-7	breast:
2	chr6:142644240..142648928-chr6:142651290..142656139,5	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1040525	0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes]
rs1040526	0.94[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs1342060	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1360194	0.94[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs1418201	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes]
rs1891308	0.87[CEU][hapmap];0.85[CHB][hapmap];0.94[EUR][1000 genomes]
rs2039986	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes]
rs2050157	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[EUR][1000 genomes]
rs2294764	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs2294771	0.86[EUR][1000 genomes]
rs3748069	0.86[EUR][1000 genomes]
rs3817929	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs4896582	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs6570507	0.87[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs6570508	0.81[EUR][1000 genomes]
rs6570509	0.94[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs6570510	0.87[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs6909857	0.94[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes]
rs6929442	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs6937121	0.94[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs7741741	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7753012	0.83[CEU][hapmap]
rs7754638	0.86[EUR][1000 genomes]
rs7755109	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs7756305	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7763064	0.83[EUR][1000 genomes]
rs7770386	0.86[EUR][1000 genomes]
rs7774095	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs7776375	0.85[EUR][1000 genomes]
rs9373346	0.87[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs9389984	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9389985	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes]
rs9389986	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[EUR][1000 genomes]
rs9389987	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9399401	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9403380	0.94[EUR][1000 genomes]
rs9403381	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403382	0.93[EUR][1000 genomes]
rs9403383	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes]
rs9403387	0.87[EUR][1000 genomes]
rs9496346	0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes]
rs9496369	0.88[EUR][1000 genomes]
rs9496374	0.88[EUR][1000 genomes]
rs9496392	0.84[EUR][1000 genomes]
rs962554	0.89[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs972982	0.81[CEU][hapmap];0.90[CHB][hapmap];0.93[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142651000-142656600	Enhancers	Liver	Liver
2	chr6:142652600-142656600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:142653000-142656000	Enhancers	HUVEC	blood vessel
4	chr6:142653000-142660800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:142653200-142657200	Enhancers	HepG2	liver
6	chr6:142653800-142656400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:142654000-142656200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:142654200-142666400	Weak transcription	HMEC	breast
9	chr6:142654200-142668800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:142654400-142656600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:142654400-142666200	Weak transcription	NHEK	skin
12	chr6:142654600-142656200	Weak transcription	NHLF	lung
13	chr6:142654800-142676600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:142655200-142655600	Enhancers	A549	lung
15	chr6:142655200-142655800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:142655400-142655600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:142655400-142655600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:142655400-142655800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:142655400-142655800	Flanking Active TSS	Fetal Lung	lung

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