Variant report

Variant	rs28468978
Chromosome Location	chr15:57153089-57153090
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MNS1-3	chr15:57151866-57153738	ENSG00000248500

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1012321	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10450961	0.86[EUR][1000 genomes]
rs11855646	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11858368	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13379960	0.89[EUR][1000 genomes]
rs1430819	0.88[EUR][1000 genomes]
rs1441236	0.91[EUR][1000 genomes]
rs1647392	0.88[EUR][1000 genomes]
rs1652744	0.81[EUR][1000 genomes]
rs1660961	0.96[EUR][1000 genomes]
rs1967352	0.82[EUR][1000 genomes]
rs1967353	0.82[EUR][1000 genomes]
rs2161933	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2163369	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2414487	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28371400	0.82[EUR][1000 genomes]
rs28568712	0.89[EUR][1000 genomes]
rs28609621	0.89[EUR][1000 genomes]
rs28736360	0.89[EUR][1000 genomes]
rs28874022	0.91[EUR][1000 genomes]
rs4313751	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56965085	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6493893	0.87[EUR][1000 genomes]
rs6493894	0.90[EUR][1000 genomes]
rs67114210	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67278720	0.83[EUR][1000 genomes]
rs67622899	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68083905	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7163302	0.87[EUR][1000 genomes]
rs7178196	0.83[AMR][1000 genomes]
rs72747165	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8026149	0.87[EUR][1000 genomes]
rs8040866	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042606	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv3401951	chr15:57151709-57176189	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28468978	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57128200-57158600	Weak transcription	Ovary	ovary
2	chr15:57135400-57164000	Weak transcription	Aorta	Aorta
3	chr15:57138600-57161800	Weak transcription	Fetal Thymus	thymus
4	chr15:57140000-57164600	Weak transcription	Pancreas	Pancrea

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