Variant report

Variant	rs12527257
Chromosome Location	chr6:13178069-13178070
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	JUND	chr6:13178050-13178244	HepG2	liver:	n/a	n/a
2	CREB1	chr6:13177838-13178395	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PHACTR1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10948524	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11757278	1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs12525914	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12528399	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869294	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16873682	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3823445	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3864309	0.84[EUR][1000 genomes]
rs3864310	0.81[EUR][1000 genomes]
rs4097413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715132	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs62385532	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9349494	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9349501	0.87[EUR][1000 genomes]
rs9349502	0.87[EUR][1000 genomes]
rs9357620	0.91[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357634	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9367368	0.87[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9367369	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9369915	0.86[EUR][1000 genomes]
rs9369916	0.89[EUR][1000 genomes]
rs9369917	0.87[EUR][1000 genomes]
rs9381807	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9381809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9381810	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9381812	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9381818	0.87[EUR][1000 genomes]
rs9381819	0.87[EUR][1000 genomes]
rs9395497	0.87[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9395520	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9463511	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12527257	HIVEP1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13153600-13178200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:13153600-13178200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:13153800-13184200	Weak transcription	Aorta	Aorta
4	chr6:13159200-13181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:13159600-13178400	Weak transcription	Right Ventricle	heart
6	chr6:13163600-13183400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:13164800-13183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:13164800-13184400	Weak transcription	Pancreas	Pancrea
9	chr6:13172800-13191800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:13174600-13180400	Weak transcription	Fetal Brain Female	brain
11	chr6:13176400-13178400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:13176400-13183800	Weak transcription	Lung	lung
13	chr6:13176400-13191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:13176600-13181400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:13177400-13178200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:13177400-13179200	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:13177800-13178400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr6:13177800-13178400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:13177800-13178400	Enhancers	Brain Anterior Caudate	brain
20	chr6:13177800-13178600	Enhancers	Fetal Heart	heart
21	chr6:13177800-13178800	Enhancers	Left Ventricle	heart
22	chr6:13177800-13179200	Enhancers	Brain Hippocampus Middle	brain
23	chr6:13178000-13178400	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr6:13178000-13178800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr6:13178000-13179200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:13178000-13179200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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