Variant report

Variant	rs2467838
Chromosome Location	chr15:45489814-45489815
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45481532..45483736-chr15:45488202..45490839,2	K562	blood:
2	chr15:45475968..45478000-chr15:45488455..45490164,2	K562	blood:
3	chr15:45457346..45461990-chr15:45488766..45494297,11	MCF-7	breast:
4	chr15:45481165..45484027-chr15:45488390..45490198,2	K562	blood:
5	chr15:45458639..45463256-chr15:45489443..45493548,9	K562	blood:
6	chr15:45489521..45491302-chr15:45567648..45569193,2	MCF-7	breast:
7	chr15:45457899..45460285-chr15:45489261..45492223,4	MCF-7	breast:
8	chr15:45472426..45475821-chr15:45489773..45493159,3	K562	blood:
9	chr15:45489158..45491324-chr15:45514071..45516738,2	K562	blood:
10	chr15:45457999..45463256-chr15:45488727..45493013,8	K562	blood:
11	chr15:45484569..45487478-chr15:45489184..45491239,2	K562	blood:
12	chr15:45489573..45492565-chr15:45693942..45696435,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171763	Chromatin interaction
ENSG00000259539	Chromatin interaction
ENSG00000259519	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000138606	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10467979	0.80[AMR][1000 genomes]
rs11634794	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11636395	0.81[AFR][1000 genomes]
rs11855466	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12323957	0.83[EUR][1000 genomes]
rs12437603	0.81[EUR][1000 genomes]
rs12438755	0.81[EUR][1000 genomes]
rs12593605	0.81[EUR][1000 genomes]
rs12899786	0.84[EUR][1000 genomes]
rs12902212	0.83[EUR][1000 genomes]
rs12904079	0.97[EUR][1000 genomes]
rs12905053	0.83[EUR][1000 genomes]
rs12905246	0.81[EUR][1000 genomes]
rs13329228	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1648287	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1648289	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1648302	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1648311	0.82[EUR][1000 genomes]
rs1648316	0.80[EUR][1000 genomes]
rs16940351	0.82[ASN][1000 genomes]
rs1706763	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1706821	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1706822	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706834	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2292467	0.82[EUR][1000 genomes]
rs2554455	0.80[AMR][1000 genomes]
rs2554456	0.80[AMR][1000 genomes]
rs2554457	0.80[AMR][1000 genomes]
rs28524974	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs28526629	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs28680861	0.84[AFR][1000 genomes]
rs3959644	0.98[EUR][1000 genomes]
rs4514617	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs58547297	0.82[ASN][1000 genomes]
rs62026661	0.95[EUR][1000 genomes]
rs62026665	0.97[EUR][1000 genomes]
rs62026666	0.91[EUR][1000 genomes]
rs7174913	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2467838	CTD-2651B20.1	cis	Artery Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45481000-45490200	Weak transcription	Ovary	ovary
2	chr15:45481000-45490600	Weak transcription	Colonic Mucosa	Colon
3	chr15:45481200-45490200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:45481200-45490400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:45482000-45490000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:45489400-45490000	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:45489400-45490000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:45489400-45490000	Enhancers	HepG2	liver
9	chr15:45489400-45490000	Enhancers	HMEC	breast
10	chr15:45489600-45490000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:45489600-45490200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:45489600-45490200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:45489600-45490200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:45489600-45490200	Enhancers	Fetal Thymus	thymus
15	chr15:45489600-45490200	Flanking Active TSS	Dnd41	blood
16	chr15:45489600-45490200	Flanking Active TSS	Hela-S3	cervix
17	chr15:45489600-45494000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:45489800-45490000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr15:45489800-45490000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:45489800-45490000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr15:45489800-45490000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr15:45489800-45490000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:45489800-45490000	Enhancers	Brain Anterior Caudate	brain
24	chr15:45489800-45490000	Flanking Active TSS	K562	blood
25	chr15:45489800-45490000	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr15:45489800-45490000	Flanking Active TSS	NHEK	skin
27	chr15:45489800-45490200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr15:45489800-45490200	Enhancers	Primary B cells from peripheral blood	blood
29	chr15:45489800-45490200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr15:45489800-45490200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr15:45489800-45490200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:45489800-45490200	Flanking Active TSS	Fetal Brain Male	brain
33	chr15:45489800-45490200	Flanking Active TSS	Fetal Brain Female	brain
34	chr15:45489800-45490200	Enhancers	Thymus	Thymus
35	chr15:45489800-45490200	Flanking Active TSS	GM12878-XiMat	blood
36	chr15:45489800-45490200	Flanking Active TSS	NHDF-Ad	bronchial
37	chr15:45489800-45490600	Weak transcription	Esophagus	oesophagus
38	chr15:45489800-45491000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:45489800-45491600	Active TSS	Fetal Intestine Small	intestine
40	chr15:45489800-45493400	Active TSS	A549	lung
41	chr15:45489800-45493600	Active TSS	H9 Cell Line	embryonic stem cell
42	chr15:45489800-45493600	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr15:45489800-45493800	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr15:45489800-45493800	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr15:45489800-45493800	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr15:45489800-45494000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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