Variant report

Variant	rs1048505
Chromosome Location	chr19:38219553-38219554
allele	G/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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF573-2	chr19:38219487-38220685	ENSG00000267152.1

Extended variants
information (count: 57 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10445548	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061756	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12150862	0.91[ASN][1000 genomes]
rs12151082	0.91[ASN][1000 genomes]
rs12151156	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244713	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244769	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17248097	0.91[ASN][1000 genomes]
rs17248670	0.91[ASN][1000 genomes]
rs17249138	0.91[ASN][1000 genomes]
rs17303902	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17304703	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305193	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305228	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305823	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17306900	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871196	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291001	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306201	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2385005	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35153242	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3859549	0.91[ASN][1000 genomes]
rs4536583	0.91[ASN][1000 genomes]
rs55681348	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55718806	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55743020	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55754546	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55865869	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55909413	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56184201	0.91[ASN][1000 genomes]
rs56233644	0.91[ASN][1000 genomes]
rs56268127	0.91[ASN][1000 genomes]
rs56277404	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56290614	0.91[ASN][1000 genomes]
rs56351266	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57654288	0.84[EUR][1000 genomes]
rs57943942	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7245855	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73031330	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033122	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033134	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033142	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73035159	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73035160	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73039029	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041006	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041036	0.91[ASN][1000 genomes]
rs8101610	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104282	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104994	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8108268	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110293	0.91[ASN][1000 genomes]
rs8111790	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1048505	AC012309.5	cis	Thyroid	GTEx
rs1048505	AC012309.5	cis	Muscle Skeletal	GTEx
rs1048505	ZNF781	cis	Thyroid	GTEx
rs1048505	AC012309.5	cis	Esophagus Muscularis	GTEx
rs1048505	AC012309.5	cis	lung	GTEx
rs1048505	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs1048505	AC012309.5	cis	Artery Tibial	GTEx
rs1048505	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs1048505	AC012309.5	cis	Esophagus Mucosa	GTEx
rs1048505	AC012309.5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:28 , 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	chr19:38211000-38222000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr19:38211000-38224600	Weak transcription	Fetal Stomach	stomach
4	chr19:38211000-38225200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr19:38211000-38225200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:38211000-38226400	Weak transcription	Psoas Muscle	Psoas
7	chr19:38211000-38227600	Weak transcription	Brain Hippocampus Middle	brain
8	chr19:38211000-38228400	Weak transcription	Fetal Muscle Leg	muscle
9	chr19:38211000-38228600	Weak transcription	Brain Substantia Nigra	brain
10	chr19:38211000-38229200	Weak transcription	Fetal Kidney	kidney
11	chr19:38211000-38229200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr19:38211000-38229200	Weak transcription	Left Ventricle	heart
13	chr19:38211000-38229400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:38211000-38229400	Weak transcription	Brain Germinal Matrix	brain
15	chr19:38211000-38229400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:38211000-38230200	Weak transcription	Hela-S3	cervix
17	chr19:38211200-38225600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr19:38211200-38229200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr19:38211200-38229200	Weak transcription	Fetal Brain Female	brain
20	chr19:38211200-38229200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:38215600-38219600	ZNF genes & repeats	Liver	Liver
22	chr19:38218200-38220600	Weak transcription	Fetal Intestine Small	intestine
23	chr19:38218400-38229200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr19:38218800-38221400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:38219000-38221400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:38219000-38221600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr19:38219400-38221800	Weak transcription	Pancreas	Pancrea
28	chr19:38219400-38224600	Weak transcription	Ovary	ovary

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