Variant report

Variant	rs7045138
Chromosome Location	chr9:100591463-100591464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100585593..100587654-chr9:100591414..100594781,4	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10046805	0.87[ASN][1000 genomes]
rs10124220	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10818124	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10818133	0.87[ASN][1000 genomes]
rs10983833	0.88[ASN][1000 genomes]
rs10983853	0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs10983855	0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs10983871	0.90[ASN][1000 genomes]
rs1156850	0.96[ASN][1000 genomes]
rs12341377	0.87[ASN][1000 genomes]
rs12347191	0.87[ASN][1000 genomes]
rs12348304	0.87[ASN][1000 genomes]
rs12348691	0.87[ASN][1000 genomes]
rs1443432	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1443434	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1443435	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1867277	0.84[ASN][1000 genomes]
rs1867278	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2401639	0.87[ASN][1000 genomes]
rs3021526	0.82[ASN][1000 genomes]
rs3758248	0.87[ASN][1000 genomes]
rs3758249	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3758251	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4297160	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460498	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6478413	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6478437	0.87[ASN][1000 genomes]
rs7033765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851552	0.87[ASN][1000 genomes]
rs7851660	0.86[ASN][1000 genomes]
rs7870540	0.96[ASN][1000 genomes]
rs7870795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs894673	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs907577	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[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	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Thyroid hormone levels	23408906	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7045138	C9orf156	cis	Frontal Cortex	GTEx
rs7045138	C9orf156	cis	Temporal Cortex	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100590600-100593200	Weak transcription	H9 Cell Line	embryonic stem cell

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