Variant report

Variant	rs6475312
Chromosome Location	chr9:19047080-19047081
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:19047048..19050954-chr9:19228997..19232024,5	K562	blood:
2	chr9:19044018..19047294-chr9:19047672..19049656,4	K562	blood:
3	chr9:19032362..19034123-chr9:19046838..19049376,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137145	Chromatin interaction
ENSG00000155875	Chromatin interaction
ENSG00000155876	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10122990	0.81[ASN][1000 genomes]
rs10123400	0.85[ASN][1000 genomes]
rs10123624	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10125646	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10125677	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1048169	0.89[ASN][1000 genomes]
rs10757024	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10757025	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10811103	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10811104	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10963921	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10963924	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10963925	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1154672	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1154673	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12236344	0.88[EUR][1000 genomes]
rs12236347	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13287117	0.84[ASN][1000 genomes]
rs13287517	0.84[ASN][1000 genomes]
rs1932457	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2130570	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2130571	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2233798	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35133951	0.85[ASN][1000 genomes]
rs4392990	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4394488	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4977278	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4977492	0.85[ASN][1000 genomes]
rs6475311	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6475313	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6475314	0.85[ASN][1000 genomes]
rs6475315	0.85[ASN][1000 genomes]
rs68092871	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7027346	0.85[ASN][1000 genomes]
rs7035738	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7036118	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7036182	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7036301	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7037772	0.90[ASN][1000 genomes]
rs7037787	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7043115	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7043507	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7045844	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7854974	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7855250	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7855338	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7856768	0.86[ASN][1000 genomes]
rs9298795	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv973452	chr9:19033958-19053096	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6475312	FAM29A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19037200-19048400	Weak transcription	Stomach Mucosa	stomach
2	chr9:19043600-19048400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:19046200-19048600	Weak transcription	Right Atrium	heart
4	chr9:19047000-19048600	Weak transcription	Psoas Muscle	Psoas

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