Variant report

Variant	rs56384860
Chromosome Location	chr3:120057382-120057383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120055227..120058044-chr3:120066812..120069506,3	MCF-7	breast:
2	chr3:120055756..120058586-chr3:120065980..120068170,2	K562	blood:
3	chr3:120054050..120055684-chr3:120056041..120057735,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163428	Chromatin interaction
ENSG00000240661	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs41271405	1.00[EUR][1000 genomes]
rs55640624	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55885326	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56048284	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56239327	1.00[EUR][1000 genomes]
rs56281929	1.00[EUR][1000 genomes]
rs58174591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58296615	1.00[EUR][1000 genomes]
rs58932850	1.00[EUR][1000 genomes]
rs59522791	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59766787	1.00[EUR][1000 genomes]
rs59779647	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60136263	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60814807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61160321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61535593	1.00[EUR][1000 genomes]
rs6764372	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72956853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72956859	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72956861	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72956897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958712	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958714	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958778	1.00[EUR][1000 genomes]
rs73855206	1.00[EUR][1000 genomes]
rs73855223	1.00[EUR][1000 genomes]
rs73855241	1.00[EUR][1000 genomes]
rs73856465	1.00[EUR][1000 genomes]
rs73856468	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
3	chr3:120033200-120060400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:120033200-120060400	Weak transcription	Pancreas	Pancrea
5	chr3:120033200-120067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:120041000-120057400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:120041000-120057400	Weak transcription	Small Intestine	intestine
8	chr3:120041000-120058000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:120042800-120060400	Weak transcription	Gastric	stomach
10	chr3:120042800-120060600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:120043200-120060400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:120044400-120066800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:120045200-120066800	Weak transcription	Stomach Mucosa	stomach
14	chr3:120045600-120066800	Weak transcription	Colonic Mucosa	Colon
15	chr3:120048400-120066800	Weak transcription	Right Ventricle	heart
16	chr3:120048600-120063000	Weak transcription	HSMMtube	muscle
17	chr3:120050400-120066000	Weak transcription	Fetal Brain Male	brain
18	chr3:120051000-120060600	Weak transcription	Spleen	Spleen
19	chr3:120051000-120063800	Weak transcription	NHLF	lung
20	chr3:120051000-120067000	Weak transcription	Esophagus	oesophagus
21	chr3:120051200-120065600	Weak transcription	HMEC	breast
22	chr3:120051200-120066800	Weak transcription	Psoas Muscle	Psoas
23	chr3:120051200-120066800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:120051800-120065600	Weak transcription	Brain Angular Gyrus	brain
25	chr3:120052000-120060400	Weak transcription	Lung	lung
26	chr3:120052000-120060800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:120052600-120067000	Weak transcription	Left Ventricle	heart
28	chr3:120052800-120057400	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:120052800-120057600	Weak transcription	Fetal Brain Female	brain
30	chr3:120052800-120064400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:120053000-120061200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:120053000-120062400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:120053000-120062800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:120053200-120059400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:120053200-120061600	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:120053200-120063000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:120053200-120065200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:120053200-120066600	Weak transcription	Fetal Kidney	kidney
39	chr3:120053800-120057400	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:120053800-120058600	Weak transcription	Fetal Stomach	stomach
41	chr3:120053800-120066600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:120053800-120066600	Weak transcription	NH-A	brain
43	chr3:120054000-120057400	Weak transcription	Liver	Liver
44	chr3:120054000-120057400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:120054000-120057400	Weak transcription	Brain Substantia Nigra	brain
46	chr3:120054000-120057400	Weak transcription	Fetal Lung	lung
47	chr3:120054000-120057400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:120054000-120057400	Weak transcription	Hela-S3	cervix
49	chr3:120054000-120057600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:120054000-120057800	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links