Variant report

Variant	rs73039029
Chromosome Location	chr19:38226066-38226067
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	chr19:38225257..38227730-chr19:38293878..38296712,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10445548	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1048505	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061753	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061756	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12150862	0.91[ASN][1000 genomes]
rs12151082	0.91[ASN][1000 genomes]
rs12151156	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244713	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244769	0.81[AMR][1000 genomes];0.81[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	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17304703	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305193	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305228	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305823	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17306900	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871196	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291001	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306201	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2385005	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35153242	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3859549	0.91[ASN][1000 genomes]
rs4536583	0.91[ASN][1000 genomes]
rs55681348	0.84[AMR][1000 genomes];0.84[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	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55754546	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55865869	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55909413	0.81[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]
rs56290614	0.91[ASN][1000 genomes]
rs56351266	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57654288	0.83[EUR][1000 genomes]
rs57943942	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245855	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73031330	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033122	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033134	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033142	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73035159	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73035160	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041036	0.91[ASN][1000 genomes]
rs8101610	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104282	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104994	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8108268	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110293	0.91[ASN][1000 genomes]
rs8111790	0.81[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs73039029	AC012309.5	cis	Heart Left Ventricle	GTEx
rs73039029	AC012309.5	cis	Esophagus Muscularis	GTEx
rs73039029	AC012309.5	cis	Artery Tibial	GTEx
rs73039029	AC012309.5	cis	Muscle Skeletal	GTEx
rs73039029	AC012309.5	cis	Thyroid	GTEx
rs73039029	AC012309.5	cis	Esophagus Mucosa	GTEx
rs73039029	ZNF781	cis	Thyroid	GTEx

Chromatin state (count:48 , 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	chr19:38211000-38226400	Weak transcription	Psoas Muscle	Psoas
3	chr19:38211000-38227600	Weak transcription	Brain Hippocampus Middle	brain
4	chr19:38211000-38228400	Weak transcription	Fetal Muscle Leg	muscle
5	chr19:38211000-38228600	Weak transcription	Brain Substantia Nigra	brain
6	chr19:38211000-38229200	Weak transcription	Fetal Kidney	kidney
7	chr19:38211000-38229200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr19:38211000-38229200	Weak transcription	Left Ventricle	heart
9	chr19:38211000-38229400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:38211000-38229400	Weak transcription	Brain Germinal Matrix	brain
11	chr19:38211000-38229400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:38211000-38230200	Weak transcription	Hela-S3	cervix
13	chr19:38211200-38229200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:38211200-38229200	Weak transcription	Fetal Brain Female	brain
15	chr19:38211200-38229200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:38218400-38229200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr19:38221200-38241800	ZNF genes & repeats	Liver	Liver
18	chr19:38223800-38227000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:38224000-38229400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:38224600-38241600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:38224800-38229200	Weak transcription	Fetal Lung	lung
22	chr19:38225200-38227200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
23	chr19:38225200-38232400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr19:38225200-38232400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:38225200-38232400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
26	chr19:38225200-38232400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr19:38225200-38232400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
28	chr19:38225200-38237200	ZNF genes & repeats	Adipose Nuclei	Adipose
29	chr19:38225400-38226600	ZNF genes & repeats	A549	lung
30	chr19:38225400-38227200	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr19:38225400-38231600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:38225400-38232400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:38225400-38232400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
34	chr19:38225600-38226600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:38225600-38227000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
36	chr19:38225600-38227600	Strong transcription	Ovary	ovary
37	chr19:38225600-38227800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:38225600-38227800	Weak transcription	Pancreas	Pancrea
39	chr19:38225600-38228000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr19:38225600-38228400	Weak transcription	Fetal Stomach	stomach
41	chr19:38225600-38229200	Weak transcription	Right Ventricle	heart
42	chr19:38225800-38226800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:38225800-38227800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:38226000-38226200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
45	chr19:38226000-38226600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
46	chr19:38226000-38227600	ZNF genes & repeats	Small Intestine	intestine
47	chr19:38226000-38228600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr19:38226000-38232200	ZNF genes & repeats	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links