Variant report

Variant	rs4687561
Chromosome Location	chr3:52902455-52902456
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	chr3:52900488..52902600-chr3:52922846..52925520,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11130329	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2336660	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2336661	1.00[YRI][hapmap]
rs2336662	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535624	0.85[AMR][1000 genomes]
rs2710336	0.81[YRI][hapmap]
rs4687681	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773441	1.00[YRI][hapmap]
rs6787916	0.85[AMR][1000 genomes]
rs6798472	1.00[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:52886200-52907800	Weak transcription	NHLF	lung
3	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
7	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
9	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
11	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:52888600-52902600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:52889800-52909400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:52890000-52907800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:52890000-52908600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:52890000-52908800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:52891600-52909400	Weak transcription	Ovary	ovary
19	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
20	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:52892200-52906000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:52892600-52903200	Weak transcription	Brain Substantia Nigra	brain
23	chr3:52892600-52907800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:52894600-52904000	Weak transcription	Pancreas	Pancrea
25	chr3:52894600-52911200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:52894800-52907600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:52895000-52909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:52895400-52904600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:52895400-52907400	Weak transcription	Brain Angular Gyrus	brain
30	chr3:52895400-52919400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:52895600-52904800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:52895800-52923800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:52895800-52925200	Weak transcription	Esophagus	oesophagus
34	chr3:52896200-52909800	Weak transcription	Gastric	stomach
35	chr3:52896400-52904400	Weak transcription	Right Ventricle	heart
36	chr3:52898400-52907400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:52898600-52904400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:52898800-52909600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:52900000-52912800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:52900200-52903600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:52900200-52905800	Weak transcription	Dnd41	blood
42	chr3:52900400-52902600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:52900400-52903200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:52900400-52903600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:52900600-52904400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:52900600-52907200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:52900600-52909000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:52900600-52912200	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:52900800-52903800	Weak transcription	Thymus	Thymus
50	chr3:52900800-52904400	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links