Variant report

Variant	rs28662502
Chromosome Location	chr15:41702510-41702511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41696803..41699662-chr15:41700695..41704414,5	MCF-7	breast:
2	chr15:41702039..41704730-chr15:41706085..41709218,4	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs28479336	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28503916	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28508151	1.00[ASN][1000 genomes]
rs28631111	1.00[ASN][1000 genomes]
rs4924549	1.00[ASN][1000 genomes]
rs72739663	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
5	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
6	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv569232	chr15:41694377-41730246	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28662502	NUSAP1	cis	cerebellar cortex	BrainEAC
rs28662502	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28662502	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28662502	NUSAP1	cis	brain	BrainEAC
rs28662502	NUSAP1	cis	intralobular white matter	BrainEAC
rs28662502	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28662502	NDUFAF1	cis	Muscle Skeletal	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41695400-41703000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:41695400-41707800	Weak transcription	HSMMtube	muscle
3	chr15:41695400-41708400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:41695600-41707600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:41695600-41707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:41695600-41708400	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:41697400-41707800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:41699200-41703400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr15:41699600-41706400	Weak transcription	HepG2	liver
10	chr15:41700600-41707600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:41700600-41707800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:41700800-41703000	Weak transcription	Stomach Mucosa	stomach
13	chr15:41700800-41703200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:41700800-41703200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:41700800-41703400	Weak transcription	NHEK	skin
16	chr15:41700800-41707600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:41700800-41707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:41701000-41708000	Weak transcription	Lung	lung
19	chr15:41701800-41703000	Enhancers	K562	blood
20	chr15:41701800-41703200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:41702000-41708200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr15:41702200-41707800	Weak transcription	A549	lung
23	chr15:41702200-41708400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:41702400-41702800	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr15:41702400-41703200	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr15:41702400-41707600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:41702400-41707800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:41702400-41707800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:41702400-41707800	Weak transcription	Fetal Intestine Large	intestine
30	chr15:41702400-41707800	Weak transcription	Fetal Intestine Small	intestine

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