Variant report

Variant	rs12347647
Chromosome Location	chr9:8396744-8396745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10976945	1.00[AMR][1000 genomes]
rs10976986	1.00[AMR][1000 genomes]
rs10977011	1.00[AMR][1000 genomes]
rs10977081	0.87[YRI][hapmap]
rs10977087	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12335734	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12335970	1.00[AMR][1000 genomes]
rs12336314	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12336360	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12337640	1.00[AMR][1000 genomes]
rs12338276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12338619	1.00[AMR][1000 genomes]
rs12338889	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12339065	1.00[AMR][1000 genomes]
rs12339710	1.00[AMR][1000 genomes]
rs12341516	1.00[AMR][1000 genomes]
rs12342740	1.00[AMR][1000 genomes]
rs12342969	1.00[AMR][1000 genomes]
rs12343245	1.00[AMR][1000 genomes]
rs12343761	1.00[AMR][1000 genomes]
rs12345027	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345077	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12345562	1.00[AMR][1000 genomes]
rs12345617	1.00[AMR][1000 genomes]
rs12346847	1.00[AMR][1000 genomes]
rs12350567	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12351899	1.00[AMR][1000 genomes]
rs12352299	1.00[AMR][1000 genomes]
rs12353003	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13439921	1.00[AMR][1000 genomes]
rs28585575	1.00[AMR][1000 genomes]
rs3903827	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7035353	1.00[AMR][1000 genomes]
rs7035451	1.00[AMR][1000 genomes]
rs7045988	1.00[AMR][1000 genomes]
rs7046946	1.00[AMR][1000 genomes]
rs7048112	1.00[AMR][1000 genomes]
rs73410514	1.00[AMR][1000 genomes]
rs73420445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73420453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73420457	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73420468	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73428153	1.00[AMR][1000 genomes]
rs7871181	1.00[AMR][1000 genomes]
rs7873894	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][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	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12347647	AHSP	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8339600-8397600	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:8361400-8401600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:8364800-8401600	Weak transcription	Brain Germinal Matrix	brain
4	chr9:8367200-8399800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:8373000-8402200	Weak transcription	Fetal Kidney	kidney
6	chr9:8376800-8401800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:8377800-8406400	Weak transcription	Fetal Brain Female	brain
8	chr9:8383600-8405200	Weak transcription	Aorta	Aorta
9	chr9:8385200-8401400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:8387800-8398800	Weak transcription	Ovary	ovary
11	chr9:8388000-8402000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:8389600-8451000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:8393800-8397400	Enhancers	Brain Cingulate Gyrus	brain
14	chr9:8394000-8424400	Weak transcription	Fetal Lung	lung
15	chr9:8394400-8397800	Enhancers	Brain Substantia Nigra	brain
16	chr9:8394600-8397200	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr9:8394800-8397400	Enhancers	Brain Hippocampus Middle	brain
18	chr9:8395000-8401800	Weak transcription	Brain Angular Gyrus	brain
19	chr9:8395600-8402000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:8395800-8401600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:8395800-8401600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr9:8396000-8410400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:8396200-8401600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:8396600-8396800	Enhancers	Brain Anterior Caudate	brain

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