Variant report

Variant	rs62108351
Chromosome Location	chr19:38215896-38215897
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	chr19:38212285..38216569-chr19:38218099..38220854,3	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1060522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853710	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666172	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668796	0.87[EUR][1000 genomes]
rs11671953	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11673497	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16975299	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17246792	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28431170	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2891657	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34991303	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55871826	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55913702	0.87[EUR][1000 genomes]
rs55950325	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108305	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6508739	0.87[EUR][1000 genomes]
rs7249622	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253081	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258385	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73037060	0.84[EUR][1000 genomes];0.81[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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62108351	AC012309.5	cis	Thyroid	GTEx
rs62108351	ZNF573	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38210800-38229400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:38211000-38219000	Weak transcription	Ovary	ovary
3	chr19:38211000-38222000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr19:38211000-38224600	Weak transcription	Fetal Stomach	stomach
5	chr19:38211000-38225200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:38211000-38225200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:38211000-38226400	Weak transcription	Psoas Muscle	Psoas
8	chr19:38211000-38227600	Weak transcription	Brain Hippocampus Middle	brain
9	chr19:38211000-38228400	Weak transcription	Fetal Muscle Leg	muscle
10	chr19:38211000-38228600	Weak transcription	Brain Substantia Nigra	brain
11	chr19:38211000-38229200	Weak transcription	Fetal Kidney	kidney
12	chr19:38211000-38229200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr19:38211000-38229200	Weak transcription	Left Ventricle	heart
14	chr19:38211000-38229400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:38211000-38229400	Weak transcription	Brain Germinal Matrix	brain
16	chr19:38211000-38229400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:38211000-38230200	Weak transcription	Hela-S3	cervix
18	chr19:38211200-38225600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr19:38211200-38229200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:38211200-38229200	Weak transcription	Fetal Brain Female	brain
21	chr19:38211200-38229200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr19:38215600-38219600	ZNF genes & repeats	Liver	Liver

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