Variant report

Variant	rs12522477
Chromosome Location	chr5:60956901-60956902
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	chr5:60238110..60240722-chr5:60956482..60958434,2	MCF-7	breast:
2	chr5:60626402..60629468-chr5:60952559..60956981,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf43-4	chr5:60955986-60956930	ucscGeneNc_uc003jss_2

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1032750	0.95[CEU][hapmap]
rs10514916	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12523615	0.83[EUR][1000 genomes]
rs12654405	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12658207	0.80[JPT][hapmap]
rs1501842	0.91[CEU][hapmap]
rs1604440	1.00[CEU][hapmap]
rs1604441	1.00[CEU][hapmap]
rs16875007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16893398	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16893470	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16893616	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16893642	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16893680	1.00[CEU][hapmap]
rs16893684	1.00[CEU][hapmap]
rs16893698	0.95[CEU][hapmap]
rs1979016	0.80[CEU][hapmap]
rs2030888	0.95[CEU][hapmap]
rs2280686	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280687	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2937831	1.00[CEU][hapmap]
rs2950220	1.00[CEU][hapmap]
rs2974452	1.00[CEU][hapmap]
rs4145723	1.00[CEU][hapmap]
rs4700422	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4700423	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700425	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4700427	0.81[EUR][1000 genomes]

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60950800-60957200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:60953600-60963000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:60955200-60974400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:60955400-60957000	Enhancers	Brain Cingulate Gyrus	brain
5	chr5:60955400-60957000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr5:60955400-60957200	Enhancers	Brain Anterior Caudate	brain
7	chr5:60955600-60962000	Weak transcription	Brain Angular Gyrus	brain
8	chr5:60956000-60962000	Weak transcription	Pancreas	Pancrea
9	chr5:60956400-60957200	Enhancers	Brain Substantia Nigra	brain
10	chr5:60956400-60963000	Weak transcription	Fetal Intestine Small	intestine
11	chr5:60956600-60957800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:60956800-60961800	Weak transcription	Brain Hippocampus Middle	brain

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