Variant report

Variant	rs12901680
Chromosome Location	chr15:49880905-49880906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10851478	0.86[AFR][1000 genomes]
rs10851479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070695	0.82[ASN][1000 genomes]
rs11634947	0.82[AFR][1000 genomes]
rs11637582	0.80[ASN][1000 genomes]
rs11852336	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11853248	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11854671	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11858411	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12050614	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12050624	0.80[ASN][1000 genomes]
rs12148716	0.92[AFR][1000 genomes]
rs12148764	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12232355	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12591317	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591659	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12593151	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12595692	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12902960	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12906134	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12906972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12907661	0.85[ASN][1000 genomes]
rs12907918	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12907944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12908624	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12908635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12912703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916839	0.80[AFR][1000 genomes]
rs1395901	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1395903	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17479589	0.89[ASN][1000 genomes]
rs1911612	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1948975	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1976551	0.85[ASN][1000 genomes]
rs2413956	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2899434	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34002493	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34146550	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34246470	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34414487	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34694913	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34941109	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35698479	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4436732	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4480740	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4547278	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4775816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55904469	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62009977	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62021589	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62022665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62022667	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493372	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7162741	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7172906	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7174135	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8032688	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8033476	0.80[ASN][1000 genomes]
rs925104	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569392	chr15:49789413-49926300	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1040578	chr15:49841444-49890789	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3445639	chr15:49879810-49882008	Weak transcription Enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases
5	esv3371348	chr15:49880410-49881458	Active TSS Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12901680	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49856200-49897400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr15:49863800-49881400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:49864800-49881600	Weak transcription	Brain Substantia Nigra	brain
4	chr15:49865400-49881400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:49865400-49881800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:49866800-49881200	Weak transcription	Primary T cells from cord blood	blood
7	chr15:49866800-49881600	Weak transcription	Pancreas	Pancrea
8	chr15:49866800-49897600	Weak transcription	Ovary	ovary
9	chr15:49867200-49881400	Weak transcription	Fetal Heart	heart
10	chr15:49868800-49892400	Weak transcription	Left Ventricle	heart
11	chr15:49879400-49881400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:49879400-49881400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:49879600-49887600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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