Variant report

Variant	rs12777258
Chromosome Location	chr10:45394961-45394962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45391583..45394476-chr10:45394730..45397519,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10736831	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10751360	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10751361	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10793564	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10793565	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10900123	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10900126	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10900127	0.80[ASN][1000 genomes]
rs10900128	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900129	0.83[ASN][1000 genomes]
rs11239271	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11239274	0.84[ASN][1000 genomes]
rs1408814	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2026428	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2065466	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2281841	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3740086	0.89[ASN][1000 genomes]
rs3740087	0.91[ASN][1000 genomes]
rs4245614	0.97[EUR][1000 genomes]
rs4268464	0.96[EUR][1000 genomes]
rs4481983	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4948645	0.96[EUR][1000 genomes]
rs4948925	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4948926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4948927	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5000415	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6593447	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7079573	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7903412	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7909074	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879073	0.96[EUR][1000 genomes]
rs879074	0.96[EUR][1000 genomes]
rs914699	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][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	nsv517161	chr10:45210690-45416256	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv831844	chr10:45228791-45407762	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv831845	chr10:45300268-45460395	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12777258	ALOX5	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45375200-45398600	Weak transcription	Right Atrium	heart
2	chr10:45387000-45398400	Weak transcription	Fetal Intestine Small	intestine
3	chr10:45391000-45399000	Weak transcription	Primary T cells from cord blood	blood
4	chr10:45394000-45395600	Enhancers	Fetal Muscle Trunk	muscle
5	chr10:45394000-45395600	Enhancers	Fetal Muscle Leg	muscle
6	chr10:45394200-45395600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:45394200-45395800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:45394200-45395800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr10:45394200-45395800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:45394200-45395800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:45394200-45396000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr10:45394400-45395800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:45394600-45395600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr10:45394600-45398400	Weak transcription	Pancreas	Pancrea
15	chr10:45394800-45395400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr10:45394800-45395600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr10:45394800-45395600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr10:45394800-45395600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr10:45394800-45395600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr10:45394800-45395800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr10:45394800-45395800	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links