Variant report

Variant	rs4964228
Chromosome Location	chr12:104572759-104572760
allele	C/T
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104530177..104533540-chr12:104569302..104573926,9	MCF-7	breast:
2	chr12:104571599..104574180-chr12:104689003..104690549,2	MCF-7	breast:
3	chr12:104571824..104574318-chr12:104580582..104582719,2	MCF-7	breast:
4	chr12:104566313..104569865-chr12:104572688..104576807,3	K562	blood:
5	chr12:104570742..104573318-chr12:104574956..104577002,2	K562	blood:
6	chr12:104565973..104567600-chr12:104571102..104573461,2	MCF-7	breast:
7	chr12:104528363..104533397-chr12:104570131..104576145,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10507174	0.84[CEU][hapmap]
rs10735392	0.93[CEU][hapmap]
rs10735393	0.93[CEU][hapmap]
rs10735395	1.00[AFR][1000 genomes]
rs10745995	0.93[CEU][hapmap]
rs10745996	0.93[CEU][hapmap]
rs10861204	0.93[CEU][hapmap];1.00[AFR][1000 genomes]
rs11111919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11111943	1.00[AFR][1000 genomes]
rs11111955	0.87[CEU][hapmap]
rs12426862	0.81[CEU][hapmap]
rs17202862	0.86[CEU][hapmap];1.00[AFR][1000 genomes]
rs3935020	1.00[AFR][1000 genomes]
rs4129598	0.93[CEU][hapmap]
rs4246264	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs4246269	0.93[CEU][hapmap]
rs4246271	0.93[CEU][hapmap];1.00[AFR][1000 genomes]
rs4388968	1.00[CEU][hapmap]
rs4545635	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs4614534	0.93[CEU][hapmap]
rs4630362	0.92[CEU][hapmap];1.00[AFR][1000 genomes]
rs4964227	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4964257	1.00[AFR][1000 genomes]
rs4964260	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs4964288	0.93[CEU][hapmap];1.00[AFR][1000 genomes]
rs4964627	0.93[CEU][hapmap]
rs4964727	0.88[EUR][1000 genomes]
rs4964729	0.81[EUR][1000 genomes]
rs4964732	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4964752	0.93[CEU][hapmap]
rs4964761	0.93[CEU][hapmap]
rs4964779	0.93[CEU][hapmap]
rs4964784	1.00[AFR][1000 genomes]
rs6539131	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6539137	0.92[CEU][hapmap];1.00[AFR][1000 genomes]
rs7132418	0.93[CEU][hapmap]
rs7138035	0.82[CEU][hapmap]
rs7138317	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs7294997	1.00[CEU][hapmap]
rs7299669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7299866	0.93[CEU][hapmap]
rs73177977	1.00[AFR][1000 genomes]
rs73177980	1.00[AFR][1000 genomes]
rs73177982	1.00[AFR][1000 genomes]
rs73177990	1.00[AFR][1000 genomes]
rs73181916	1.00[AFR][1000 genomes]
rs73181919	1.00[AFR][1000 genomes]
rs73181926	1.00[AFR][1000 genomes]
rs73181944	1.00[AFR][1000 genomes]
rs7957725	0.93[CEU][hapmap]
rs7962423	0.93[CEU][hapmap]
rs7969604	1.00[AFR][1000 genomes]
rs9738614	1.00[AFR][1000 genomes]
rs9739826	1.00[AFR][1000 genomes]
rs9739833	0.93[CEU][hapmap]

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	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104566400-104573400	Weak transcription	Spleen	Spleen
2	chr12:104570000-104573000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:104570800-104572800	Enhancers	Rectal Smooth Muscle	rectum
4	chr12:104571000-104573000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:104571000-104573200	Enhancers	Colon Smooth Muscle	Colon
6	chr12:104571000-104576600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:104572000-104572800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:104572200-104572800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:104572200-104572800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:104572200-104572800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:104572200-104572800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:104572200-104574200	Weak transcription	Aorta	Aorta
13	chr12:104572200-104574400	Weak transcription	Adipose Nuclei	Adipose
14	chr12:104572200-104574400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:104572200-104574400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:104572200-104574800	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:104572200-104575200	Weak transcription	Fetal Lung	lung
18	chr12:104572200-104575600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:104572200-104575800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:104572200-104576000	Weak transcription	Right Atrium	heart
21	chr12:104572400-104573400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:104572400-104573600	Enhancers	A549	lung
23	chr12:104572400-104574600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:104572400-104574600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:104572400-104575000	Weak transcription	NH-A	brain
26	chr12:104572400-104575000	Weak transcription	NHDF-Ad	bronchial
27	chr12:104572400-104575200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:104572400-104576000	Weak transcription	Ovary	ovary
29	chr12:104572600-104572800	Enhancers	Osteobl	bone
30	chr12:104572600-104573000	Enhancers	Hela-S3	cervix
31	chr12:104572600-104574000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:104572600-104574200	Weak transcription	HMEC	breast
33	chr12:104572600-104574200	Weak transcription	NHLF	lung
34	chr12:104572600-104574800	Weak transcription	Placenta	Placenta
35	chr12:104572600-104575200	Weak transcription	HSMMtube	muscle
36	chr12:104572600-104576200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links