Variant report

Variant	rs1731947
Chromosome Location	chr7:137081525-137081526
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1367593	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1431093	0.81[JPT][hapmap]
rs161340	0.84[ASN][1000 genomes]
rs161341	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161342	0.88[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161344	0.84[ASN][1000 genomes]
rs161345	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1669025	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs167668	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1731951	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs178612	0.84[ASN][1000 genomes]
rs192935	0.83[ASN][1000 genomes]
rs192936	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2599356	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs320684	0.87[ASN][1000 genomes]
rs320686	0.91[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs320687	0.84[ASN][1000 genomes]
rs320689	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs320690	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs320691	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs320692	0.87[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs320693	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs320694	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs320695	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs320697	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs725838	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869820	chr7:136990386-137347718	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1027868	chr7:137004690-137311653	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv539134	chr7:137004690-137311653	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1731947	AC078842.3	cis	Thyroid	GTEx
rs1731947	PTN	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137066200-137084800	Weak transcription	HSMM	muscle
2	chr7:137070200-137087000	Weak transcription	Brain Angular Gyrus	brain
3	chr7:137071000-137083400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:137073600-137086600	Weak transcription	Fetal Brain Female	brain
5	chr7:137073800-137095600	Weak transcription	HSMMtube	muscle
6	chr7:137074000-137084800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:137074400-137084000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:137075000-137087000	Weak transcription	Brain Anterior Caudate	brain
9	chr7:137075200-137084800	Weak transcription	Fetal Heart	heart
10	chr7:137076000-137087000	Weak transcription	Fetal Stomach	stomach
11	chr7:137077800-137086400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:137078600-137082000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr7:137079200-137082000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:137080600-137082000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:137080600-137086400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:137080600-137106000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:137081000-137086600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:137081000-137086600	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:137081200-137081800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:137081200-137082200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:137081200-137086600	Weak transcription	Brain Substantia Nigra	brain
22	chr7:137081200-137087200	Weak transcription	Brain Germinal Matrix	brain
23	chr7:137081200-137090000	Weak transcription	Aorta	Aorta
24	chr7:137081400-137084400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:137081400-137084800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr7:137081400-137084800	Weak transcription	Osteobl	bone

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