Variant report

Variant	rs10948524
Chromosome Location	chr6:13188493-13188494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11757278	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[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]
rs12528399	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16869294	1.00[ASW][hapmap];0.87[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs16873682	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3778646	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3823445	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3864309	0.85[EUR][1000 genomes]
rs3864310	0.82[EUR][1000 genomes]
rs4097413	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4715132	0.91[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs62385532	0.91[EUR][1000 genomes]
rs9349494	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9349501	0.89[EUR][1000 genomes]
rs9349502	0.89[EUR][1000 genomes]
rs9357620	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs9357634	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9367368	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9367369	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369915	0.88[EUR][1000 genomes]
rs9369916	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369917	0.89[EUR][1000 genomes]
rs9381807	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9381809	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9381810	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9381812	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9381818	0.89[EUR][1000 genomes]
rs9381819	0.89[EUR][1000 genomes]
rs9395497	0.87[ASW][hapmap];0.91[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9395520	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9463511	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3326413	chr6:13185696-13191025	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10948524	HIVEP1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13172800-13191800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:13176400-13191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:13178800-13191400	Weak transcription	Left Ventricle	heart
4	chr6:13178800-13217400	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:13181600-13190600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:13182000-13205400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:13182000-13211800	Weak transcription	Fetal Brain Female	brain
8	chr6:13182000-13212000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:13182000-13230000	Weak transcription	Brain Angular Gyrus	brain
10	chr6:13182200-13192800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:13182800-13188600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:13183000-13195200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:13183000-13207000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:13184000-13188600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:13184000-13190600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:13184000-13220800	Weak transcription	Brain Germinal Matrix	brain
17	chr6:13184200-13197000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:13185000-13191600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:13185000-13202800	Weak transcription	Brain Anterior Caudate	brain
20	chr6:13185200-13191400	Weak transcription	Right Ventricle	heart
21	chr6:13185200-13204000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr6:13185200-13205200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:13185400-13192400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:13185400-13204800	Weak transcription	Lung	lung
25	chr6:13185400-13205800	Weak transcription	Aorta	Aorta
26	chr6:13185400-13205800	Weak transcription	Pancreas	Pancrea
27	chr6:13185600-13188600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:13185800-13191600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr6:13187400-13217400	Weak transcription	Right Atrium	heart
30	chr6:13187600-13188600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:13187600-13191200	Weak transcription	Fetal Heart	heart
32	chr6:13187800-13192600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:13188200-13189000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:13188400-13189200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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