Variant report

Variant	rs28744401
Chromosome Location	chr4:119989901-119989902
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119988837..119992890-chr4:120132998..120134761,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction
ENSG00000178636	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10017724	0.90[EUR][1000 genomes]
rs10020899	0.91[EUR][1000 genomes]
rs10021107	0.91[EUR][1000 genomes]
rs1047894	0.91[EUR][1000 genomes]
rs1058449	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1058451	0.91[EUR][1000 genomes]
rs1459063	0.91[EUR][1000 genomes]
rs17050108	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17050116	0.91[EUR][1000 genomes]
rs17050123	0.91[EUR][1000 genomes]
rs17265233	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17330453	0.89[ASN][1000 genomes]
rs28411116	0.91[EUR][1000 genomes]
rs28493971	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495816	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28560056	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28609814	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28698789	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756153	0.91[EUR][1000 genomes]
rs62326862	0.82[ASN][1000 genomes]
rs62328679	0.91[EUR][1000 genomes]
rs62328680	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328681	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328710	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328715	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328716	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328720	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992697	0.80[EUR][1000 genomes]
rs9998313	0.91[EUR][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised 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 miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119967400-119994000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr4:119975800-119994000	Weak transcription	Right Ventricle	heart
3	chr4:119975800-120003000	Weak transcription	Left Ventricle	heart
4	chr4:119979200-119996400	Weak transcription	Aorta	Aorta
5	chr4:119980600-119994000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:119988800-119992200	Enhancers	HepG2	liver
7	chr4:119988800-119992600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:119989000-119990200	Enhancers	Rectal Smooth Muscle	rectum
9	chr4:119989200-119990000	Flanking Active TSS	NHEK	skin
10	chr4:119989200-119992600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:119989400-119990000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:119989400-119990000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:119989400-119990200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:119989400-119990200	Enhancers	Osteobl	bone
15	chr4:119989400-119990400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:119989400-119990400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr4:119989400-119990400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:119989400-119990400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr4:119989400-119992400	Enhancers	HMEC	breast
20	chr4:119989600-119990000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr4:119989600-119990000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:119989600-119990000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr4:119989600-119990400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:119989600-119990400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:119989600-119990400	Enhancers	Colon Smooth Muscle	Colon
26	chr4:119989600-119990800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:119989600-119990800	Weak transcription	Esophagus	oesophagus
28	chr4:119989600-119991000	Enhancers	H1 Cell Line	embryonic stem cell
29	chr4:119989600-119992800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:119989800-119990000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr4:119989800-119990000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr4:119989800-119990200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr4:119989800-119990400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr4:119989800-119990400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:119989800-119990400	Enhancers	A549	lung
36	chr4:119989800-119990800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:119989800-119990800	Weak transcription	Placenta	Placenta
38	chr4:119989800-119990800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr4:119989800-119991600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr4:119989800-119991800	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links