Variant report

Variant	rs59564034
Chromosome Location	chr3:51613542-51613543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51532821..51534762-chr3:51612325..51614079,2	K562	blood:

Variant related genes	Relation type
ENSG00000145041	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12485610	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12486568	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487426	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12490471	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12492624	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12493265	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12493618	0.81[EUR][1000 genomes]
rs12493857	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12494462	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12496340	0.93[EUR][1000 genomes]
rs13089799	0.87[EUR][1000 genomes]
rs13090348	0.87[EUR][1000 genomes]
rs13324384	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17051811	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2033703	0.87[EUR][1000 genomes]
rs2082992	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2082993	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2356298	0.83[ASN][1000 genomes]
rs35536327	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687553	1.00[EUR][1000 genomes]
rs4687563	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687592	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4687599	0.87[EUR][1000 genomes]
rs4687605	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687656	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687691	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4687769	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4687794	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55667499	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55701928	0.85[AFR][1000 genomes]
rs55706150	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55760693	0.80[AFR][1000 genomes]
rs55872019	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56239081	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56729479	0.83[ASN][1000 genomes]
rs57027950	0.87[EUR][1000 genomes]
rs58059174	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58189274	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58762652	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59838596	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60007226	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60606339	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61233013	0.86[ASN][1000 genomes]
rs61689323	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72951443	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72951490	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7375146	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73834253	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73834254	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73834258	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73834265	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9827186	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9842600	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9843583	0.94[EUR][1000 genomes];0.83[ASN][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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51574000-51615400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:51574000-51624800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:51574200-51616400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:51574400-51613800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:51574600-51624600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:51574800-51624800	Weak transcription	NH-A	brain
7	chr3:51575200-51615600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:51578800-51624400	Weak transcription	Esophagus	oesophagus
9	chr3:51584200-51614200	Weak transcription	Aorta	Aorta
10	chr3:51585000-51615600	Weak transcription	NHEK	skin
11	chr3:51585200-51624400	Weak transcription	Brain Germinal Matrix	brain
12	chr3:51585800-51625000	Weak transcription	Colonic Mucosa	Colon
13	chr3:51587800-51624400	Weak transcription	Hela-S3	cervix
14	chr3:51588000-51640000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:51593600-51615600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:51594000-51615600	Weak transcription	Osteobl	bone
17	chr3:51594200-51622800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:51594200-51622800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:51597200-51622800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:51598400-51622800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:51598600-51614200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:51600800-51654600	Weak transcription	Stomach Mucosa	stomach
23	chr3:51601000-51615400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:51601000-51624600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:51601200-51640000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:51602200-51615600	Weak transcription	NHDF-Ad	bronchial
27	chr3:51602400-51615600	Weak transcription	K562	blood
28	chr3:51602400-51622800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:51602800-51615600	Weak transcription	Brain Angular Gyrus	brain
30	chr3:51602800-51615600	Weak transcription	Left Ventricle	heart
31	chr3:51602800-51615600	Weak transcription	HSMMtube	muscle
32	chr3:51602800-51619200	Weak transcription	Brain Anterior Caudate	brain
33	chr3:51602800-51619200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:51602800-51622800	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:51602800-51624400	Weak transcription	NHLF	lung
36	chr3:51602800-51628200	Weak transcription	Small Intestine	intestine
37	chr3:51602800-51643800	Weak transcription	Right Atrium	heart
38	chr3:51603200-51615600	Weak transcription	Fetal Heart	heart
39	chr3:51603200-51619400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:51603200-51622800	Weak transcription	HSMM	muscle
41	chr3:51603200-51624400	Weak transcription	Right Ventricle	heart
42	chr3:51603400-51615600	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:51603400-51619200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:51607600-51613800	Weak transcription	Dnd41	blood
45	chr3:51607600-51615800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:51607600-51622800	Weak transcription	Adipose Nuclei	Adipose
47	chr3:51607600-51624600	Weak transcription	GM12878-XiMat	blood
48	chr3:51607800-51613800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:51607800-51614000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:51607800-51614000	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links