Variant report

Variant	rs3776481
Chromosome Location	chr5:73982695-73982696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:73969331..73972056-chr5:73981357..73983781,2	MCF-7	breast:
2	chr5:73981038..73983852-chr5:73999852..74002635,2	MCF-7	breast:
3	chr5:73980885..73983030-chr5:74062980..74064496,2	MCF-7	breast:
4	chr5:73981324..73983563-chr5:74077397..74079724,2	K562	blood:
5	chr5:73981661..73984902-chr5:74226605..74228461,3	K562	blood:
6	chr5:73980953..73983731-chr5:74012002..74014571,3	MCF-7	breast:
7	chr5:73979743..73983565-chr5:73984545..73990071,12	K562	blood:

Variant related genes	Relation type
ENSG00000239517	Chromatin interaction
ENSG00000049860	Chromatin interaction
ENSG00000164346	Chromatin interaction
ENSG00000164347	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10515187	0.82[ASN][1000 genomes]
rs10805890	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10942716	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10942717	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11738401	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11738782	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11738805	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11746583	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11747100	0.81[ASN][1000 genomes]
rs11747317	0.81[ASN][1000 genomes]
rs11748221	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11749103	0.89[ASN][1000 genomes]
rs11749435	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11750605	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11750634	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11750747	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12233980	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12233981	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16872198	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17670514	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3894712	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4460123	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59514206	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6898989	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7445920	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13844	chr5:73979961-73993853	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
2	nsv598652	chr5:73980182-73992881	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv934214	chr5:73981349-73993050	Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv933165	chr5:73981599-73993050	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73980600-73982800	Active TSS	Fetal Kidney	kidney
2	chr5:73980800-73982800	Active TSS	Fetal Intestine Large	intestine
3	chr5:73981400-73982800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr5:73981400-73983000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr5:73981400-73983200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr5:73981400-73983200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:73981400-73983200	Flanking Active TSS	Dnd41	blood
8	chr5:73981600-73983000	Enhancers	Fetal Heart	heart
9	chr5:73981600-73983000	Flanking Active TSS	Osteobl	bone
10	chr5:73981600-73983400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:73981600-73983400	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr5:73981600-73983400	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr5:73981600-73983400	Flanking Active TSS	Hela-S3	cervix
14	chr5:73981800-73982800	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr5:73981800-73982800	Flanking Active TSS	HMEC	breast
16	chr5:73981800-73983000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:73981800-73983200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:73981800-73983200	Enhancers	Spleen	Spleen
19	chr5:73981800-73983400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:73981800-73983400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr5:73981800-73983400	Flanking Active TSS	NHLF	lung
22	chr5:73982000-73982800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr5:73982000-73983000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr5:73982000-73983000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:73982000-73983000	Transcr. at gene 5' and 3'	K562	blood
26	chr5:73982000-73983200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:73982000-73983200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:73982000-73983200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:73982000-73983200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr5:73982000-73983200	Enhancers	Small Intestine	intestine
31	chr5:73982000-73983200	Flanking Active TSS	GM12878-XiMat	blood
32	chr5:73982000-73983200	Flanking Active TSS	NHDF-Ad	bronchial
33	chr5:73982000-73983400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:73982000-73983400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr5:73982000-73983400	Enhancers	Right Atrium	heart
36	chr5:73982000-73983400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr5:73982000-73988800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:73982000-73989000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr5:73982000-73994400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:73982000-74002200	Weak transcription	Fetal Brain Female	brain
41	chr5:73982000-74017400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:73982200-73982800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:73982200-73982800	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr5:73982200-73983000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr5:73982200-73983000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr5:73982200-73983000	Enhancers	Colon Smooth Muscle	Colon
48	chr5:73982200-73983200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr5:73982200-73983200	Enhancers	Aorta	Aorta
50	chr5:73982200-73983200	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links