Variant report

Variant	rs12973580
Chromosome Location	chr19:38408994-38408995
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	chr19:38407792..38410171-chr19:38481203..38483917,2	MCF-7	breast:
2	chr19:38402813..38405228-chr19:38408699..38411381,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10404159	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10415399	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10415548	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11083441	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12608883	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1643460	0.81[EUR][1000 genomes]
rs1643461	0.85[EUR][1000 genomes]
rs1725499	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28460297	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs353410	0.90[EUR][1000 genomes]
rs353411	0.90[EUR][1000 genomes]
rs3786869	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4239516	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4802144	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802147	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802151	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4803551	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803573	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs705491	0.90[EUR][1000 genomes]
rs705493	0.90[EUR][1000 genomes]
rs705495	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs705499	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8108434	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109053	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109835	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8113273	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8113521	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12973580	AC012309.5	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
2	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:38399000-38418400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:38399000-38422400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:38399200-38409400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:38399200-38411000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:38399200-38411000	Weak transcription	Stomach Mucosa	stomach
8	chr19:38399200-38411400	Weak transcription	NHEK	skin
9	chr19:38399200-38411800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:38399200-38411800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr19:38399200-38415600	Weak transcription	Hela-S3	cervix
12	chr19:38399200-38416000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:38399200-38422400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr19:38399200-38422600	Weak transcription	Fetal Lung	lung
15	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:38399600-38409600	Weak transcription	NHLF	lung
17	chr19:38399600-38411400	Weak transcription	Esophagus	oesophagus
18	chr19:38399600-38422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
21	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:38399800-38409600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:38399800-38409600	Weak transcription	Brain Anterior Caudate	brain
24	chr19:38399800-38410800	Weak transcription	Brain Angular Gyrus	brain
25	chr19:38399800-38411000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:38399800-38411000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:38399800-38411600	Weak transcription	Lung	lung
28	chr19:38399800-38413800	Weak transcription	Liver	Liver
29	chr19:38399800-38417200	Weak transcription	Ovary	ovary
30	chr19:38399800-38421200	Weak transcription	Gastric	stomach
31	chr19:38399800-38421800	Weak transcription	Left Ventricle	heart
32	chr19:38399800-38422400	Weak transcription	Fetal Brain Female	brain
33	chr19:38399800-38422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr19:38400000-38411200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:38400000-38411400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr19:38400000-38422000	Weak transcription	HSMM	muscle
37	chr19:38400400-38409600	Weak transcription	Dnd41	blood
38	chr19:38400400-38409600	Weak transcription	NHDF-Ad	bronchial
39	chr19:38400400-38411000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:38400400-38411200	Weak transcription	Brain Germinal Matrix	brain
41	chr19:38400400-38416800	Weak transcription	Pancreas	Pancrea
42	chr19:38400400-38419400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr19:38400400-38421800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:38400600-38409800	Weak transcription	Fetal Intestine Large	intestine
45	chr19:38400600-38410000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:38400600-38411400	Weak transcription	Osteobl	bone
47	chr19:38400600-38422000	Weak transcription	HSMMtube	muscle
48	chr19:38400600-38422400	Weak transcription	HUVEC	blood vessel
49	chr19:38400800-38409600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:38400800-38411400	Weak transcription	NH-A	brain

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