Variant report

Variant	rs28460297
Chromosome Location	chr19:38416453-38416454
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38415914..38418453-chr19:38418940..38421267,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10404159	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415399	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10415548	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083441	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1119229	0.81[EUR][1000 genomes]
rs12608883	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12973580	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1643460	0.84[EUR][1000 genomes]
rs1643461	0.88[EUR][1000 genomes]
rs1725499	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353410	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs353411	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3786869	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4239516	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802144	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802147	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802151	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4803551	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803573	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705491	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs705493	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs705495	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705499	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8108434	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109053	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109835	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8113273	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8113521	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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
rs28460297	AC012309.5	cis	Artery Tibial	GTEx

Chromatin state (count:103 , 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	chr19:38399200-38422400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr19:38399200-38422600	Weak transcription	Fetal Lung	lung
7	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:38399600-38422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
11	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:38399800-38417200	Weak transcription	Ovary	ovary
13	chr19:38399800-38421200	Weak transcription	Gastric	stomach
14	chr19:38399800-38421800	Weak transcription	Left Ventricle	heart
15	chr19:38399800-38422400	Weak transcription	Fetal Brain Female	brain
16	chr19:38399800-38422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr19:38400000-38422000	Weak transcription	HSMM	muscle
18	chr19:38400400-38416800	Weak transcription	Pancreas	Pancrea
19	chr19:38400400-38419400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:38400400-38421800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr19:38400600-38422000	Weak transcription	HSMMtube	muscle
22	chr19:38400600-38422400	Weak transcription	HUVEC	blood vessel
23	chr19:38400800-38422400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr19:38401000-38416600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:38401000-38421600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr19:38401200-38416800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:38401200-38421200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr19:38402000-38416800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:38402000-38422600	Weak transcription	Fetal Brain Male	brain
30	chr19:38404200-38416800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr19:38405200-38422600	Weak transcription	Right Ventricle	heart
32	chr19:38405600-38422800	Weak transcription	Colon Smooth Muscle	Colon
33	chr19:38406000-38416600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:38406000-38417200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr19:38406000-38418800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr19:38406000-38419400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr19:38406000-38422600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:38406400-38418200	Weak transcription	Fetal Heart	heart
39	chr19:38406400-38418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr19:38406400-38419200	Weak transcription	Colonic Mucosa	Colon
41	chr19:38407200-38417400	Genic enhancers	Primary B cells from peripheral blood	blood
42	chr19:38410200-38416600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr19:38410200-38422200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:38410200-38422400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr19:38410400-38422400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:38411600-38419400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:38411600-38422600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr19:38411800-38421200	Weak transcription	NHEK	skin
49	chr19:38411800-38422200	Weak transcription	Brain Angular Gyrus	brain
50	chr19:38411800-38422200	Weak transcription	NH-A	brain

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