Variant report

Variant	rs56357549
Chromosome Location	chr3:52374516-52374517
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52321953..52324136-chr3:52373095..52375238,2	MCF-7	breast:
2	chr3:52361669..52364614-chr3:52373969..52375582,2	K562	blood:
3	chr3:52277680..52279387-chr3:52372909..52375320,2	K562	blood:

Variant related genes	Relation type
ENSG00000168237	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10460962	0.93[AFR][1000 genomes]
rs10461028	0.90[AFR][1000 genomes]
rs1077142	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11705963	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11706001	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706108	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11707864	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707931	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709658	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710014	0.87[AFR][1000 genomes]
rs11711934	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11714402	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11716017	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718125	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs123598	1.00[ASN][1000 genomes]
rs123602	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs123603	1.00[ASN][1000 genomes]
rs13059674	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13060192	1.00[ASN][1000 genomes]
rs13075370	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076508	1.00[ASN][1000 genomes]
rs13076890	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13089892	1.00[ASN][1000 genomes]
rs13091360	1.00[ASN][1000 genomes]
rs13091545	0.90[EUR][1000 genomes]
rs13096571	1.00[ASN][1000 genomes]
rs17052053	0.94[AFR][1000 genomes]
rs17052054	0.92[AFR][1000 genomes]
rs17052058	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17052061	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17052068	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016575	0.85[EUR][1000 genomes]
rs2109557	1.00[ASN][1000 genomes]
rs2335640	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28481563	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2878549	1.00[ASN][1000 genomes]
rs34181173	1.00[ASN][1000 genomes]
rs34238085	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34332947	1.00[ASN][1000 genomes]
rs34355561	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523877	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34628357	1.00[ASN][1000 genomes]
rs34762015	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34827613	1.00[ASN][1000 genomes]
rs34908451	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35133416	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35860312	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35982798	1.00[ASN][1000 genomes]
rs3752819	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796343	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs390802	0.93[EUR][1000 genomes]
rs419050	1.00[ASN][1000 genomes]
rs419604	1.00[ASN][1000 genomes]
rs419752	1.00[ASN][1000 genomes]
rs498778	1.00[ASN][1000 genomes]
rs498946	0.89[EUR][1000 genomes]
rs55965068	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55997317	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56352611	0.94[AFR][1000 genomes]
rs57441156	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs575476	1.00[ASN][1000 genomes]
rs59612757	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61150019	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61734640	1.00[ASN][1000 genomes]
rs6445385	0.87[AFR][1000 genomes]
rs6445386	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66462821	0.90[EUR][1000 genomes]
rs67248391	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763882	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67834575	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794675	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795333	1.00[ASN][1000 genomes]
rs6796333	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6800707	0.82[EUR][1000 genomes]
rs71297391	1.00[ASN][1000 genomes]
rs71297394	1.00[ASN][1000 genomes]
rs71297395	1.00[ASN][1000 genomes]
rs71297396	1.00[ASN][1000 genomes]
rs73088800	0.94[AFR][1000 genomes]
rs7615405	0.89[AFR][1000 genomes]
rs7643570	0.90[EUR][1000 genomes]
rs82825	0.88[EUR][1000 genomes]
rs9844183	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9861879	0.81[AMR][1000 genomes];0.91[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	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
2	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
4	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:52352000-52379800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:52352200-52379000	Weak transcription	Colonic Mucosa	Colon
5	chr3:52352200-52382000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:52352200-52384600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:52352600-52379400	Weak transcription	Pancreas	Pancrea
8	chr3:52353400-52377400	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:52354400-52379800	Weak transcription	Esophagus	oesophagus
10	chr3:52354800-52384000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:52358400-52380400	Weak transcription	Ovary	ovary
12	chr3:52360400-52376200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:52362200-52375000	Weak transcription	Fetal Thymus	thymus
14	chr3:52362400-52378200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:52362800-52378600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:52364200-52375800	Weak transcription	GM12878-XiMat	blood
17	chr3:52364200-52383000	Weak transcription	Fetal Lung	lung
18	chr3:52364400-52379400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:52364800-52394400	Weak transcription	HSMMtube	muscle
20	chr3:52366400-52378400	Weak transcription	Brain Anterior Caudate	brain
21	chr3:52366400-52383000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:52366600-52375200	Weak transcription	Lung	lung
23	chr3:52366600-52377800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:52366600-52377800	Weak transcription	Spleen	Spleen
25	chr3:52366600-52378400	Weak transcription	Gastric	stomach
26	chr3:52366600-52379400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:52366600-52386600	Weak transcription	Aorta	Aorta
28	chr3:52366800-52383000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:52367200-52378600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:52367200-52379600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:52367600-52384400	Weak transcription	Fetal Kidney	kidney
32	chr3:52367800-52375800	Weak transcription	Fetal Stomach	stomach
33	chr3:52368400-52375000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:52368400-52376200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:52368400-52378400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:52368400-52378400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:52368400-52378600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:52368400-52383000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:52368600-52375000	Weak transcription	Fetal Intestine Large	intestine
40	chr3:52368800-52375000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:52368800-52377000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:52368800-52377400	Weak transcription	Adipose Nuclei	Adipose
43	chr3:52368800-52377600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:52368800-52378200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:52368800-52378200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:52368800-52378400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:52368800-52380200	Weak transcription	Left Ventricle	heart
48	chr3:52368800-52380400	Weak transcription	Placenta	Placenta
49	chr3:52368800-52380400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:52370600-52379600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links