Variant report

Variant	rs28375864
Chromosome Location	chr4:148915992-148915993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148912653..148914620-chr4:148915114..148916621,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10008133	1.00[AMR][1000 genomes]
rs10008249	1.00[AMR][1000 genomes]
rs10008590	1.00[AMR][1000 genomes]
rs10009344	1.00[AMR][1000 genomes]
rs10010607	1.00[AMR][1000 genomes]
rs10012283	1.00[AMR][1000 genomes]
rs10012907	1.00[AMR][1000 genomes]
rs10025355	0.83[AFR][1000 genomes]
rs10029241	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10031581	1.00[AMR][1000 genomes]
rs10032952	1.00[AMR][1000 genomes]
rs10034151	1.00[AMR][1000 genomes]
rs17024101	1.00[EUR][1000 genomes]
rs17024109	1.00[EUR][1000 genomes]
rs2037480	1.00[AMR][1000 genomes]
rs28377573	1.00[AMR][1000 genomes]
rs28391722	1.00[AMR][1000 genomes]
rs28500506	1.00[AMR][1000 genomes]
rs28519574	1.00[AMR][1000 genomes]
rs28522552	1.00[EUR][1000 genomes]
rs28529145	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28544401	1.00[AMR][1000 genomes]
rs28549338	1.00[AMR][1000 genomes]
rs28572262	1.00[AMR][1000 genomes]
rs28592193	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28594565	1.00[EUR][1000 genomes]
rs28615270	1.00[AMR][1000 genomes]
rs28633738	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28637907	1.00[EUR][1000 genomes]
rs28672384	1.00[AMR][1000 genomes]
rs28687202	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28696003	1.00[AMR][1000 genomes]
rs28716209	1.00[EUR][1000 genomes]
rs28759001	1.00[AMR][1000 genomes]
rs28837820	1.00[AMR][1000 genomes]
rs28886306	1.00[AMR][1000 genomes]
rs36114707	1.00[EUR][1000 genomes]
rs57726071	1.00[EUR][1000 genomes]
rs59333422	1.00[EUR][1000 genomes]
rs59532898	1.00[EUR][1000 genomes]
rs60042934	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61012783	1.00[EUR][1000 genomes]
rs61764246	1.00[EUR][1000 genomes]
rs72957750	1.00[EUR][1000 genomes]
rs73853714	1.00[AMR][1000 genomes]
rs73853989	1.00[EUR][1000 genomes]
rs73855926	1.00[AMR][1000 genomes]
rs9996205	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997923	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148866400-148927400	Weak transcription	Thymus	Thymus
2	chr4:148885600-148939000	Weak transcription	Pancreas	Pancrea
3	chr4:148886000-148917600	Weak transcription	Esophagus	oesophagus
4	chr4:148889200-148936200	Weak transcription	Fetal Intestine Large	intestine
5	chr4:148891600-148920600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:148891600-148928000	Weak transcription	A549	lung
7	chr4:148896600-148928400	Weak transcription	Spleen	Spleen
8	chr4:148897200-148917600	Weak transcription	Lung	lung
9	chr4:148898200-148920600	Weak transcription	NHEK	skin
10	chr4:148898200-148925400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:148905800-148918000	Weak transcription	Stomach Mucosa	stomach
12	chr4:148906000-148925200	Weak transcription	Adipose Nuclei	Adipose
13	chr4:148906400-148928400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:148906600-148917600	Weak transcription	Gastric	stomach
15	chr4:148906600-148920600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:148906600-148920600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:148906600-148920800	Weak transcription	Fetal Intestine Small	intestine
18	chr4:148906800-148918000	Weak transcription	NHLF	lung
19	chr4:148907200-148928000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:148907400-148928400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:148907800-148920600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:148910200-148928400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:148911600-148936200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:148911800-148917600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:148911800-148925200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:148912400-148916600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:148912600-148916600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr4:148913000-148920000	Weak transcription	GM12878-XiMat	blood
29	chr4:148913200-148916000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:148913200-148929200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:148913600-148917600	Weak transcription	Right Atrium	heart
32	chr4:148913600-148920600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:148913600-148933200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:148913800-148917200	Weak transcription	Psoas Muscle	Psoas
35	chr4:148914000-148916800	Enhancers	Fetal Heart	heart
36	chr4:148914400-148918000	Enhancers	Colon Smooth Muscle	Colon
37	chr4:148914600-148916000	Enhancers	HSMMtube	muscle
38	chr4:148914600-148916200	Enhancers	Fetal Stomach	stomach
39	chr4:148914600-148916800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:148914600-148916800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr4:148914800-148916400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr4:148914800-148916600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:148915000-148916600	Enhancers	Osteobl	bone
44	chr4:148915000-148917200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr4:148915200-148928200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:148915400-148916000	Enhancers	Right Ventricle	heart
47	chr4:148915400-148916200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr4:148915400-148916400	Flanking Active TSS	HUVEC	blood vessel
49	chr4:148915400-148916600	Enhancers	Ovary	ovary
50	chr4:148915400-148917600	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links