Variant report

Variant	rs12518152
Chromosome Location	chr5:60563883-60563884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr5:60563882-60563948	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60555601..60558433-chr5:60563419..60566177,2	K562	blood:
2	chr5:60562038..60564106-chr5:60564910..60567550,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249279	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10037643	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10052765	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10062338	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10065444	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071763	0.96[ASN][1000 genomes]
rs10434526	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471510	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10939888	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10939890	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10939892	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10939893	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12189426	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12523278	0.84[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12696979	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12696980	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13167234	0.85[AMR][1000 genomes]
rs13167244	0.85[AMR][1000 genomes]
rs13167246	0.84[AMR][1000 genomes]
rs13175564	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13187871	0.85[AMR][1000 genomes]
rs34439016	1.00[ASN][1000 genomes]
rs35310874	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129437	0.82[ASN][1000 genomes]
rs4400074	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4441832	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4540126	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4699974	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699975	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700415	0.85[AMR][1000 genomes]
rs6864367	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6867268	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6867417	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6885499	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6892128	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7448844	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7705381	0.83[AFR][1000 genomes]
rs7737448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9291718	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12518152	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60550400-60573400	Weak transcription	Gastric	stomach
2	chr5:60556000-60570200	Weak transcription	HSMM	muscle
3	chr5:60558000-60566400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:60560000-60569200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:60560400-60569400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:60560600-60564400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:60560600-60564400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:60560600-60564400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:60560600-60569000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:60560800-60571200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:60561000-60569000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:60561000-60573200	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:60562000-60564400	Weak transcription	HUVEC	blood vessel
14	chr5:60562000-60565400	Weak transcription	Stomach Mucosa	stomach
15	chr5:60563000-60567400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr5:60563800-60564400	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links