Variant report

Variant	rs9886064
Chromosome Location	chr7:78921208-78921209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10246925	0.92[AFR][1000 genomes]
rs10248245	0.86[AFR][1000 genomes]
rs10254141	0.86[YRI][hapmap]
rs10254566	0.97[AFR][1000 genomes]
rs10257920	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10258316	1.00[YRI][hapmap]
rs10264527	0.92[YRI][hapmap]
rs10265495	0.86[AFR][1000 genomes]
rs10270882	0.92[AFR][1000 genomes]
rs10278164	1.00[YRI][hapmap]
rs10441342	1.00[YRI][hapmap]
rs28379793	0.92[AFR][1000 genomes]
rs28513656	0.92[AFR][1000 genomes]
rs28553964	0.86[AFR][1000 genomes]
rs28694694	0.94[AFR][1000 genomes]
rs55653170	0.94[AFR][1000 genomes]
rs58778670	0.97[AFR][1000 genomes]
rs73704120	0.92[AFR][1000 genomes]
rs73704122	0.97[AFR][1000 genomes]
rs73704148	0.92[AFR][1000 genomes]
rs73707603	0.94[AFR][1000 genomes]
rs73707609	0.94[AFR][1000 genomes]
rs7776852	1.00[YRI][hapmap]
rs7791778	1.00[YRI][hapmap]
rs954896	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9655826	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1029799	chr7:78608097-79061737	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv831041	chr7:78819499-78973222	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2764028	chr7:78874740-79112630	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9886064	SDC1	trans	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78912000-78922200	Weak transcription	Brain Angular Gyrus	brain
2	chr7:78913800-78922400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:78913800-78923000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr7:78918200-78922200	Weak transcription	Adipose Nuclei	Adipose
5	chr7:78918400-78922200	Weak transcription	Brain Substantia Nigra	brain
6	chr7:78918600-78922200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:78919800-78921600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:78919800-78923800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:78919800-78923800	Enhancers	Osteobl	bone
10	chr7:78919800-78924000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr7:78919800-78924000	Enhancers	HMEC	breast
12	chr7:78919800-78924000	Enhancers	NHEK	skin
13	chr7:78920000-78921800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:78920600-78921400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:78920600-78924000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:78920800-78922200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:78920800-78922200	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:78921000-78921400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:78921000-78922000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:78921000-78922200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:78921000-78922200	Weak transcription	NH-A	brain
22	chr7:78921000-78922200	Weak transcription	NHLF	lung
23	chr7:78921000-78923200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:78921200-78922200	Enhancers	A549	lung

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