Variant report

Variant	rs588132
Chromosome Location	chr12:121024066-121024067
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	chr12:121021974..121024111-chr12:121148529..121150037,2	MCF-7	breast:
2	chr12:121018584..121021388-chr12:121022313..121024823,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167272	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10849755	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1167695	0.82[EUR][1000 genomes]
rs1167700	0.87[ASN][1000 genomes]
rs1167703	0.84[ASN][1000 genomes]
rs1167725	0.84[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1167726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1167727	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12307148	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12310837	1.00[CEU][hapmap]
rs1614223	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1671767	0.81[ASN][1000 genomes]
rs17431717	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs1794748	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1794749	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2235222	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2673618	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4347449	0.89[ASN][1000 genomes]
rs550876	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs563920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567156	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs580016	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs591992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs616157	0.84[EUR][1000 genomes]
rs640350	0.86[EUR][1000 genomes]
rs7137953	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs7174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405622	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787824	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs787827	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs787832	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956998	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963543	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs7972244	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv973944	chr12:121017088-121027122	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs588132	POP5	cis	Lymphoblastoid	GTEx
rs588132	POP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121019600-121027200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:121022800-121026200	Weak transcription	Right Ventricle	heart
3	chr12:121022800-121026600	Weak transcription	Left Ventricle	heart
4	chr12:121022800-121026800	Weak transcription	Psoas Muscle	Psoas
5	chr12:121022800-121027000	Weak transcription	Brain Anterior Caudate	brain
6	chr12:121022800-121028800	Weak transcription	Esophagus	oesophagus
7	chr12:121023000-121026000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:121023000-121026200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:121023000-121026600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:121023000-121026600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:121023000-121027000	Weak transcription	Colonic Mucosa	Colon
12	chr12:121023000-121027400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:121023400-121024400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
14	chr12:121023800-121024400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:121024000-121024200	Bivalent Enhancer	Brain Germinal Matrix	brain

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