Variant report

Variant	rs12135605
Chromosome Location	chr1:95787058-95787059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RWDD3-2	chr1:95786850-95787167	XLOC_000308
2	lnc-RWDD3-1	chr1:95786849-95787167	NONHSAT004662

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10874912	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874914	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11165366	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165367	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165374	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11165375	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11165379	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116466	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12118116	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12141215	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12142805	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12565207	0.83[EUR][1000 genomes]
rs12752448	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1548278	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17589093	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182021	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2893323	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34009737	0.85[AMR][1000 genomes]
rs34988332	0.90[AMR][1000 genomes]
rs4129611	0.90[AMR][1000 genomes]
rs4359066	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4394708	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4408199	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4604740	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61771812	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66930640	0.90[AMR][1000 genomes]
rs72723875	0.92[AMR][1000 genomes]
rs912648	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs927703	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[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	nsv830648	chr1:95760162-95926264	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1006113	chr1:95768502-96139003	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv529002	chr1:95781217-95805002	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12135605	TMEM56	cis	cerebellum	SCAN
rs12135605	OR8B4	trans	cerebellum	SCAN
rs12135605	FAM69A	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95786600-95787400	Active TSS	Brain Anterior Caudate	brain
2	chr1:95786600-95787400	Active TSS	Brain Hippocampus Middle	brain
3	chr1:95786800-95787200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:95786800-95787200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:95786800-95787200	Flanking Active TSS	Brain Germinal Matrix	brain
6	chr1:95786800-95787200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:95786800-95787200	Active TSS	Fetal Brain Female	brain
8	chr1:95786800-95787200	Flanking Active TSS	Fetal Lung	lung
9	chr1:95786800-95787200	Active TSS	NHDF-Ad	bronchial
10	chr1:95786800-95787400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr1:95786800-95787400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:95786800-95787400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:95786800-95787400	Active TSS	Brain Angular Gyrus	brain
14	chr1:95786800-95787400	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:95786800-95787800	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr1:95786800-95789200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:95786800-95789600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:95787000-95787200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr1:95787000-95787200	Flanking Active TSS	Brain Substantia Nigra	brain
20	chr1:95787000-95787800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:95787000-95787800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:95787000-95788200	Enhancers	Fetal Brain Male	brain
23	chr1:95787000-95789400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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