Variant report

Variant	rs11757278
Chromosome Location	chr6:13180454-13180455
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	chr6:13180442-13180470	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PHACTR1	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10948524	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12525914	0.95[CEU][hapmap]
rs12527257	1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs12528399	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16869294	0.87[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs16869298	0.83[YRI][hapmap]
rs16873682	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3778646	1.00[CEU][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs3823445	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3864309	0.81[EUR][1000 genomes]
rs3864310	0.84[EUR][1000 genomes]
rs4097413	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715132	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs62385532	0.89[EUR][1000 genomes]
rs6922797	0.91[YRI][hapmap]
rs6934799	0.91[YRI][hapmap]
rs6935948	0.81[LWK][hapmap];0.91[YRI][hapmap]
rs9349494	1.00[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs9349501	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9349502	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357620	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs9357634	0.88[EUR][1000 genomes]
rs9367368	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9367369	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9369915	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369916	0.87[EUR][1000 genomes]
rs9369917	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9381807	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9381809	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9381810	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9381812	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9381818	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9381819	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395497	0.91[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs9395520	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9463511	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][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	nsv600992	chr6:12961922-13218549	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	nsv883450	chr6:13166341-13196011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11757278	PHACTR1	cis	multi-tissue	Pritchard
rs11757278	HIVEP1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13153800-13184200	Weak transcription	Aorta	Aorta
2	chr6:13159200-13181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:13163600-13183400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:13164800-13183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:13164800-13184400	Weak transcription	Pancreas	Pancrea
6	chr6:13172800-13191800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:13176400-13183800	Weak transcription	Lung	lung
8	chr6:13176400-13191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:13176600-13181400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:13178400-13184400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:13178600-13181400	Weak transcription	Brain Angular Gyrus	brain
12	chr6:13178600-13183800	Weak transcription	Fetal Heart	heart
13	chr6:13178800-13180800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:13178800-13181200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:13178800-13181400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:13178800-13182000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr6:13178800-13184000	Weak transcription	Right Ventricle	heart
18	chr6:13178800-13187200	Weak transcription	Spleen	Spleen
19	chr6:13178800-13191400	Weak transcription	Left Ventricle	heart
20	chr6:13178800-13217400	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:13179000-13180600	Weak transcription	Brain Anterior Caudate	brain
22	chr6:13179000-13181200	Weak transcription	Brain Substantia Nigra	brain
23	chr6:13179000-13181400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:13179200-13181400	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:13179200-13184800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:13179800-13181000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:13180400-13180800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:13180400-13180800	Enhancers	Brain Germinal Matrix	brain
29	chr6:13180400-13181400	Enhancers	Fetal Brain Female	brain
30	chr6:13180400-13182200	Enhancers	Primary hematopoietic stem cells	blood

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