Variant report

Variant	rs1502800
Chromosome Location	chr12:86476255-86476256
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10779231	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs10863135	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs10863146	0.81[CEU][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap]
rs10863149	0.85[CEU][hapmap]
rs10863162	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863163	0.93[YRI][hapmap]
rs11117146	0.81[CEU][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap]
rs11513957	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs12298174	0.86[YRI][hapmap]
rs12301701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12308575	0.95[YRI][hapmap]
rs12318815	0.92[JPT][hapmap]
rs1354258	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393612	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1502799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6539935	0.81[CEU][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap]
rs6539941	0.81[ASN][1000 genomes]
rs6539942	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs7136697	0.89[YRI][hapmap]
rs7300073	0.83[JPT][hapmap]
rs7301280	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7305869	0.81[CEU][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap]
rs7313373	0.81[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap]
rs7313442	0.81[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap]
rs7314272	0.81[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap]
rs7397730	0.94[GIH][hapmap];1.00[JPT][hapmap]
rs7485285	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7955173	1.00[JPT][hapmap]
rs7966352	0.94[GIH][hapmap];0.92[JPT][hapmap]
rs7975457	0.81[CEU][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap]
rs7978562	0.89[ASW][hapmap];0.81[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs8181635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap]
rs839146	0.82[MEX][hapmap]
rs865720	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs952851	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];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv832476	chr12:86389751-86497122	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3345033	chr12:86458294-86514745	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1502800	TMTC3	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86473800-86476400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:86473800-86476400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:86473800-86477000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:86474400-86476400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr12:86475000-86476400	Enhancers	Brain Cingulate Gyrus	brain
6	chr12:86475400-86476400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:86475400-86476600	Enhancers	Brain Germinal Matrix	brain
8	chr12:86476200-86477200	Weak transcription	Brain Inferior Temporal Lobe	brain

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