Variant report

Variant	rs12523278
Chromosome Location	chr5:60563907-60563908
allele	A/G
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: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10037643	0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10052765	0.87[ASN][1000 genomes]
rs10062338	0.87[ASN][1000 genomes]
rs10065444	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10071763	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10434526	0.92[ASN][1000 genomes]
rs10461467	0.84[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10471510	0.91[ASN][1000 genomes]
rs10939888	0.89[ASN][1000 genomes]
rs10939890	0.89[ASN][1000 genomes]
rs10939892	0.84[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10939893	0.83[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12189426	0.89[ASN][1000 genomes]
rs12513581	0.81[AMR][1000 genomes]
rs12518152	0.84[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12696979	0.87[ASN][1000 genomes]
rs12696980	0.89[ASN][1000 genomes]
rs13175564	0.84[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs34439016	0.92[ASN][1000 genomes]
rs35310874	0.92[ASN][1000 genomes]
rs4352559	0.82[TSI][hapmap]
rs4391122	0.88[YRI][hapmap]
rs4400074	0.92[ASN][1000 genomes]
rs4441832	0.92[ASN][1000 genomes]
rs4540126	0.89[ASN][1000 genomes]
rs4546329	0.82[TSI][hapmap]
rs4604142	0.83[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4699974	0.87[ASN][1000 genomes]
rs4699975	0.87[ASN][1000 genomes]
rs62366215	0.83[AMR][1000 genomes]
rs6449528	0.81[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs6864367	0.87[ASN][1000 genomes]
rs6867268	0.91[ASN][1000 genomes]
rs6867417	0.86[ASN][1000 genomes]
rs6868457	0.81[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs6885499	0.87[ASN][1000 genomes]
rs6892128	0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7448844	0.87[ASN][1000 genomes]
rs7701440	0.83[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7724551	0.83[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7737448	0.84[CHB][hapmap];0.89[ASN][1000 genomes]
rs9291718	0.86[JPT][hapmap];0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12523278	DEPDC1B	cis	cerebellum	SCAN
rs12523278	ERCC8	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

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