Variant report

Variant	rs12620195
Chromosome Location	chr2:54897125-54897126
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54896291..54898011-chr2:54946547..54949509,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1027950	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1052820	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12467653	0.84[AFR][1000 genomes]
rs12473338	0.84[AFR][1000 genomes]
rs12475342	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12611806	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12615589	0.81[EUR][1000 genomes]
rs12622340	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1510612	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17046153	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17416284	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1848923	0.81[EUR][1000 genomes]
rs2007020	0.83[ASN][1000 genomes]
rs3796012	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3817163	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671229	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4671964	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4671965	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671966	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671968	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56898160	0.83[ASN][1000 genomes]
rs59871921	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6705756	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6738725	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72618663	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72618665	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72618667	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72618668	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12620195	EML6	cis	Artery Tibial	GTEx
rs12620195	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54841200-54897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:54846600-54898000	Strong transcription	Dnd41	blood
3	chr2:54861800-54898600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:54862600-54898400	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr2:54863000-54898600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:54863000-54899400	Strong transcription	Primary T cells from cord blood	blood
7	chr2:54863800-54897400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:54863800-54898600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:54865400-54898400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:54865800-54898200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:54866400-54897200	Strong transcription	Primary B cells from cord blood	blood
12	chr2:54867200-54897800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr2:54867200-54898200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:54868800-54898600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:54869600-54898600	Strong transcription	Fetal Thymus	thymus
16	chr2:54869800-54897600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:54879600-54898400	Strong transcription	GM12878-XiMat	blood
18	chr2:54880200-54898400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr2:54880200-54898400	Strong transcription	Thymus	Thymus
20	chr2:54883000-54899400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:54889200-54898600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:54890800-54898200	Genic enhancers	Brain Inferior Temporal Lobe	brain
23	chr2:54891000-54899400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:54891200-54899800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:54891600-54898000	Genic enhancers	Brain Hippocampus Middle	brain
26	chr2:54891800-54897800	Genic enhancers	NHLF	lung
27	chr2:54892000-54897600	Genic enhancers	Fetal Lung	lung
28	chr2:54892000-54897800	Genic enhancers	Brain Cingulate Gyrus	brain
29	chr2:54892200-54897600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:54892400-54897800	Genic enhancers	Brain Substantia Nigra	brain
31	chr2:54892400-54897800	Genic enhancers	NHDF-Ad	bronchial
32	chr2:54892400-54898000	Genic enhancers	Rectal Smooth Muscle	rectum
33	chr2:54892400-54898200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:54892400-54898200	Genic enhancers	Adipose Nuclei	Adipose
35	chr2:54893000-54897200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
36	chr2:54893000-54898600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:54893200-54897400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:54893200-54898000	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr2:54893200-54898600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:54893200-54898600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:54893200-54898800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:54893400-54897600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:54893400-54898600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr2:54893800-54898600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:54893800-54899600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:54893800-54900200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:54894000-54898600	Strong transcription	HUVEC	blood vessel
48	chr2:54894000-54899400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:54894000-54899600	Strong transcription	NH-A	brain
50	chr2:54894200-54898000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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