Variant report

Variant	rs12614238
Chromosome Location	chr2:205486644-205486645
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:205475661..205477885-chr2:205486352..205487926,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10084275	0.84[EUR][1000 genomes]
rs10170405	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10174747	0.86[EUR][1000 genomes]
rs10175139	0.83[EUR][1000 genomes]
rs10198136	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10490268	0.88[EUR][1000 genomes]
rs10804143	0.94[AFR][1000 genomes]
rs10932077	0.84[EUR][1000 genomes]
rs10932079	0.87[EUR][1000 genomes]
rs10932080	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11674084	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11675511	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11675555	0.86[EUR][1000 genomes]
rs12474673	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12474806	0.87[EUR][1000 genomes]
rs12621708	0.85[AFR][1000 genomes]
rs12621786	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12694004	0.88[EUR][1000 genomes]
rs12986544	0.87[EUR][1000 genomes]
rs13017644	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13024650	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1447497	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs1861766	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1868068	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2111447	0.86[EUR][1000 genomes]
rs2193449	0.87[EUR][1000 genomes]
rs2193450	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2197691	0.90[CEU][hapmap];0.80[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2216318	0.86[EUR][1000 genomes]
rs2216319	0.84[EUR][1000 genomes]
rs2334802	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4673307	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6713748	0.82[EUR][1000 genomes]
rs6721452	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6731575	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7568847	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7587284	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7590330	0.87[EUR][1000 genomes]
rs7595939	0.87[EUR][1000 genomes]
rs7600675	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7603507	0.87[EUR][1000 genomes]
rs7609521	0.88[EUR][1000 genomes]
rs763832	0.88[EUR][1000 genomes]
rs9283519	0.85[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	nsv998485	chr2:205407813-206184006	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536122	chr2:205407813-206184006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875722	chr2:205462099-205572718	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12614238	FZD5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:205477000-205491800	Weak transcription	Fetal Lung	lung
2	chr2:205481200-205493600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:205481400-205501000	Weak transcription	Aorta	Aorta
4	chr2:205481600-205494200	Weak transcription	Fetal Brain Male	brain
5	chr2:205482200-205493800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:205482600-205486800	Weak transcription	Pancreas	Pancrea
7	chr2:205484000-205486800	Weak transcription	Right Atrium	heart
8	chr2:205484000-205493000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:205484000-205493800	Weak transcription	HSMM	muscle
10	chr2:205485400-205486800	Enhancers	Colon Smooth Muscle	Colon
11	chr2:205485600-205490000	Weak transcription	Ovary	ovary
12	chr2:205485800-205486800	Enhancers	Stomach Smooth Muscle	stomach
13	chr2:205486000-205499200	Weak transcription	Fetal Intestine Small	intestine
14	chr2:205486400-205486800	Enhancers	Stomach Mucosa	stomach
15	chr2:205486400-205487200	Enhancers	Fetal Intestine Large	intestine
16	chr2:205486600-205486800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:205486600-205487000	Enhancers	Gastric	stomach
18	chr2:205486600-205487200	Enhancers	HUVEC	blood vessel

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