Variant report

Variant	rs4924399
Chromosome Location	chr15:40177769-40177770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40166842..40170366-chr15:40176074..40178554,3	MCF-7	breast:
2	chr15:40169561..40171300-chr15:40175960..40178021,2	K562	blood:
3	chr15:40177423..40181071-chr15:40224799..40228084,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128829	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12373003	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28376567	0.86[ASN][1000 genomes]
rs28495043	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28573294	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41487846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41497851	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4923844	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55859027	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62002527	0.96[ASN][1000 genomes]
rs62002531	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62002533	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62002534	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv832983	chr15:40098766-40248839	Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40162400-40187000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:40169600-40178600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:40171600-40178600	Weak transcription	NH-A	brain
4	chr15:40173600-40178000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr15:40174800-40178800	Weak transcription	NHLF	lung
6	chr15:40175200-40178600	Weak transcription	NHDF-Ad	bronchial
7	chr15:40175600-40178400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
8	chr15:40176000-40178600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr15:40176000-40179000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr15:40176000-40180800	Enhancers	HMEC	breast
11	chr15:40176000-40182200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:40176000-40182600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr15:40176200-40177800	Enhancers	Hela-S3	cervix
14	chr15:40176200-40178000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:40176200-40180000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr15:40176200-40180600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:40176200-40182400	Enhancers	H9 Cell Line	embryonic stem cell
18	chr15:40176200-40183800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr15:40176200-40185000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr15:40176400-40178200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:40176400-40179200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:40176600-40179200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:40176800-40178000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:40176800-40178200	Enhancers	Liver	Liver
25	chr15:40176800-40181000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:40177000-40178000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:40177000-40178400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:40177000-40180400	Weak transcription	Pancreas	Pancrea
29	chr15:40177000-40180600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:40177000-40180800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:40177000-40183000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:40177200-40178000	Weak transcription	NHEK	skin
33	chr15:40177200-40178400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:40177200-40178600	Weak transcription	Osteobl	bone
35	chr15:40177200-40179400	Weak transcription	Stomach Mucosa	stomach
36	chr15:40177200-40179400	Weak transcription	HSMM	muscle
37	chr15:40177200-40179800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:40177200-40180200	Weak transcription	HSMMtube	muscle
39	chr15:40177400-40180400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr15:40177600-40177800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr15:40177600-40177800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:40177600-40179200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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