Variant report

Variant	rs8113273
Chromosome Location	chr19:38405177-38405178
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38404240..38406383-chr19:38422399..38424441,2	MCF-7	breast:
2	chr19:38399136..38401318-chr19:38404847..38407238,2	MCF-7	breast:
3	chr19:38403265..38407111-chr19:38419790..38421668,3	MCF-7	breast:
4	chr19:38402813..38405228-chr19:38408699..38411381,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10404159	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10415399	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10415548	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11083441	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1119229	0.81[EUR][1000 genomes]
rs12608883	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12973580	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1643460	0.84[EUR][1000 genomes]
rs1643461	0.88[EUR][1000 genomes]
rs1725499	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28460297	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353410	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs353411	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3786869	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4239516	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802144	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802147	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802151	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4803551	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803573	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705491	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs705493	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs705495	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705499	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8108434	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109053	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109835	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8113521	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][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
rs8113273	AC012309.5	cis	Artery Tibial	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
2	chr19:38398800-38405200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:38399000-38418400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:38399000-38422400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:38399200-38405400	Weak transcription	Adipose Nuclei	Adipose
7	chr19:38399200-38405400	Weak transcription	Fetal Muscle Leg	muscle
8	chr19:38399200-38405400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:38399200-38409400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr19:38399200-38411000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:38399200-38411000	Weak transcription	Stomach Mucosa	stomach
12	chr19:38399200-38411400	Weak transcription	NHEK	skin
13	chr19:38399200-38411800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:38399200-38411800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:38399200-38415600	Weak transcription	Hela-S3	cervix
16	chr19:38399200-38416000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:38399200-38422400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:38399200-38422600	Weak transcription	Fetal Lung	lung
19	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:38399400-38405400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr19:38399600-38405400	Weak transcription	Colonic Mucosa	Colon
22	chr19:38399600-38409600	Weak transcription	NHLF	lung
23	chr19:38399600-38411400	Weak transcription	Esophagus	oesophagus
24	chr19:38399600-38422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
27	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:38399800-38405200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr19:38399800-38405400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:38399800-38405400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:38399800-38405600	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:38399800-38405600	Weak transcription	Spleen	Spleen
33	chr19:38399800-38409600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:38399800-38409600	Weak transcription	Brain Anterior Caudate	brain
35	chr19:38399800-38410800	Weak transcription	Brain Angular Gyrus	brain
36	chr19:38399800-38411000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:38399800-38411000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:38399800-38411600	Weak transcription	Lung	lung
39	chr19:38399800-38413800	Weak transcription	Liver	Liver
40	chr19:38399800-38417200	Weak transcription	Ovary	ovary
41	chr19:38399800-38421200	Weak transcription	Gastric	stomach
42	chr19:38399800-38421800	Weak transcription	Left Ventricle	heart
43	chr19:38399800-38422400	Weak transcription	Fetal Brain Female	brain
44	chr19:38399800-38422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr19:38400000-38405200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr19:38400000-38405600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:38400000-38411200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:38400000-38411400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr19:38400000-38422000	Weak transcription	HSMM	muscle
50	chr19:38400400-38405200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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