Variant report

Variant	rs12209291
Chromosome Location	chr6:23705464-23705465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10456277	0.96[EUR][1000 genomes]
rs10456278	0.96[EUR][1000 genomes]
rs10456279	0.96[EUR][1000 genomes]
rs10946615	0.85[EUR][1000 genomes]
rs10946617	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964821	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12191024	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12191124	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12191169	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12198734	0.96[EUR][1000 genomes]
rs12198796	0.96[EUR][1000 genomes]
rs12205517	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12207724	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12210770	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12212370	0.96[EUR][1000 genomes]
rs12212408	0.96[EUR][1000 genomes]
rs12212513	0.96[EUR][1000 genomes]
rs12214844	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13202207	0.96[EUR][1000 genomes]
rs13216480	0.96[EUR][1000 genomes]
rs34217675	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34322312	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34444313	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34911525	0.96[EUR][1000 genomes]
rs35148131	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35466548	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35750020	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35776872	0.96[EUR][1000 genomes]
rs4593349	0.80[CEU][hapmap]
rs6456565	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6456570	0.91[ASN][1000 genomes]
rs6900150	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6921301	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6929007	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6930955	0.83[ASN][1000 genomes]
rs6931060	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9356874	0.84[AMR][1000 genomes];0.85[EUR][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	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv462656	chr6:23629281-23721032	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv601125	chr6:23629281-23721032	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv1027773	chr6:23644898-23776497	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3442143	chr6:23686264-23978363	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12209291	TDP2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:23704200-23706000	Enhancers	Fetal Heart	heart
2	chr6:23704400-23706200	Enhancers	Fetal Muscle Leg	muscle
3	chr6:23704400-23706600	Enhancers	Rectal Smooth Muscle	rectum
4	chr6:23704800-23705600	Enhancers	Fetal Muscle Trunk	muscle
5	chr6:23705400-23705600	Enhancers	Left Ventricle	heart
6	chr6:23705400-23705800	Weak transcription	Colon Smooth Muscle	Colon

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