Variant report

Variant	rs11048300
Chromosome Location	chr12:25998070-25998071
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IFLTD1-6	chr12:25996617-25999441	l_620_chr12:25988876-25991960_brain

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10431264	1.00[CHB][hapmap]
rs10505985	1.00[ASN][1000 genomes]
rs10505986	1.00[ASN][1000 genomes]
rs10842623	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10842624	0.94[EUR][1000 genomes]
rs10842627	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842630	1.00[ASN][1000 genomes]
rs10842634	1.00[ASN][1000 genomes]
rs10842635	1.00[ASN][1000 genomes]
rs10842636	1.00[ASN][1000 genomes]
rs10842637	1.00[ASN][1000 genomes]
rs11048289	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11048302	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11048303	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11048304	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11048305	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11048309	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11048311	1.00[ASN][1000 genomes]
rs11048312	1.00[ASN][1000 genomes]
rs11048315	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11048317	1.00[ASN][1000 genomes]
rs11048319	1.00[ASN][1000 genomes]
rs11048323	1.00[ASN][1000 genomes]
rs11048325	1.00[ASN][1000 genomes]
rs11048326	1.00[ASN][1000 genomes]
rs11048328	1.00[ASN][1000 genomes]
rs11048329	1.00[ASN][1000 genomes]
rs11048330	1.00[ASN][1000 genomes]
rs11048331	1.00[ASN][1000 genomes]
rs12227123	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12230489	0.81[EUR][1000 genomes]
rs12306745	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12313050	0.96[EUR][1000 genomes]
rs12368327	1.00[ASN][1000 genomes]
rs12369495	1.00[ASN][1000 genomes]
rs1462717	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1511008	1.00[ASN][1000 genomes]
rs16929496	0.88[AFR][1000 genomes]
rs2341292	1.00[ASN][1000 genomes]
rs56245229	1.00[ASN][1000 genomes]
rs58294161	1.00[ASN][1000 genomes]
rs66520255	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7134325	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73086135	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73086136	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73086141	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088111	1.00[ASN][1000 genomes]
rs7953149	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758300	chr12:25992331-26161116	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759886	chr12:25992331-26161116	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11048300	TMTC1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25997000-25998200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:25997200-26003800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:25997600-25998200	Enhancers	HUES48 Cell Line	embryonic stem cell

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