Variant report

Variant	rs2412478
Chromosome Location	chr15:40361172-40361173
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40357794..40362220-chr15:40389488..40392528,3	MCF-7	breast:
2	chr15:40335759..40338053-chr15:40359943..40362529,2	MCF-7	breast:
3	chr15:40352649..40354633-chr15:40358305..40361225,2	K562	blood:
4	chr15:40359476..40364618-chr15:40393648..40401523,12	MCF-7	breast:
5	chr15:40347622..40350963-chr15:40359226..40362584,4	MCF-7	breast:
6	chr15:40359906..40361762-chr15:40381062..40383010,2	MCF-7	breast:
7	chr15:40360380..40363301-chr15:40385509..40387691,4	MCF-7	breast:
8	chr15:40355457..40358717-chr15:40360057..40366974,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000104081	Chromatin interaction
ENSG00000248508	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1010879	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070250	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11631442	1.00[ASN][1000 genomes]
rs16924528	1.00[ASN][1000 genomes]
rs17722502	1.00[ASN][1000 genomes]
rs17722526	1.00[ASN][1000 genomes]
rs17723133	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28444847	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515996	1.00[ASN][1000 genomes]
rs28736699	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28826672	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35781999	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923235	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4497657	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924410	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924413	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924417	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62004114	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62004158	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71132133	1.00[ASN][1000 genomes]
rs7183977	1.00[ASN][1000 genomes]
rs72731415	1.00[ASN][1000 genomes]
rs7497289	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749748	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026641	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937213	1.00[ASN][1000 genomes]
rs9919974	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh 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

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40346000-40367400	Weak transcription	K562	blood
2	chr15:40346200-40372800	Weak transcription	Fetal Kidney	kidney
3	chr15:40348600-40365800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:40348800-40365400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:40353800-40361600	Weak transcription	Gastric	stomach
6	chr15:40355800-40361200	Weak transcription	Brain Substantia Nigra	brain
7	chr15:40355800-40361400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:40356200-40361600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:40356600-40361400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:40356600-40361400	Weak transcription	Placenta	Placenta
11	chr15:40356600-40361400	Weak transcription	Right Atrium	heart
12	chr15:40356600-40361400	Weak transcription	Right Ventricle	heart
13	chr15:40356600-40362000	Weak transcription	Brain Anterior Caudate	brain
14	chr15:40357000-40361600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:40357200-40361200	Weak transcription	Fetal Brain Male	brain
16	chr15:40357400-40361600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:40357400-40361800	Weak transcription	Brain Angular Gyrus	brain
18	chr15:40357600-40361400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:40357600-40361400	Weak transcription	Primary B cells from cord blood	blood
20	chr15:40357600-40361400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:40357600-40361400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:40357600-40365800	Weak transcription	Primary T cells from cord blood	blood
23	chr15:40358000-40361600	Enhancers	Hela-S3	cervix
24	chr15:40358000-40362600	Enhancers	A549	lung
25	chr15:40358600-40362400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:40358800-40362800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:40359000-40362600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:40359000-40368000	Weak transcription	Ovary	ovary
29	chr15:40359200-40361400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:40359200-40362200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:40359400-40361400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:40359400-40361400	Weak transcription	Thymus	Thymus
33	chr15:40359400-40361600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:40359400-40362800	Enhancers	Liver	Liver
35	chr15:40359400-40364400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:40359800-40366000	Enhancers	Fetal Thymus	thymus
37	chr15:40360200-40362200	Enhancers	Fetal Lung	lung
38	chr15:40360200-40362400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:40360200-40362600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:40360400-40361600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr15:40360400-40362000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:40360400-40362200	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr15:40360400-40362200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:40360400-40362400	Enhancers	Brain Germinal Matrix	brain
45	chr15:40360400-40362600	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr15:40360400-40362600	Enhancers	Duodenum Mucosa	Duodenum
47	chr15:40360400-40362800	Enhancers	Primary B cells from peripheral blood	blood
48	chr15:40360400-40362800	Enhancers	Fetal Muscle Leg	muscle
49	chr15:40360400-40362800	Enhancers	Lung	lung
50	chr15:40360400-40362800	Enhancers	Rectal Mucosa Donor 31	rectum

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