Variant report

Variant	rs1724577
Chromosome Location	chr15:52689631-52689632
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10518683	1.00[GIH][hapmap]
rs10518688	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12913979	1.00[EUR][1000 genomes]
rs13329278	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs13329417	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13329500	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1669870	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1669872	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs16964891	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16964903	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964910	1.00[JPT][hapmap]
rs16964924	0.93[ASN][1000 genomes]
rs16964927	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964928	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs16964935	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16964944	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16964952	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1724599	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs1724600	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs1724602	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs2222656	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2414145	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs2600903	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2600904	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693456	0.84[AFR][1000 genomes]
rs28366864	1.00[ASN][1000 genomes]
rs28367508	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28415069	0.93[ASN][1000 genomes]
rs28415349	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28415472	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28421476	0.87[ASN][1000 genomes]
rs28426997	1.00[ASN][1000 genomes]
rs28444393	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28462026	1.00[ASN][1000 genomes]
rs28475475	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs28479614	0.93[ASN][1000 genomes]
rs28480975	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28485251	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28488423	1.00[ASN][1000 genomes]
rs28499517	0.87[ASN][1000 genomes]
rs28514341	0.93[ASN][1000 genomes]
rs28515624	0.93[ASN][1000 genomes]
rs28534436	1.00[ASN][1000 genomes]
rs28538563	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28564655	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28590330	1.00[ASN][1000 genomes]
rs28594692	0.93[ASN][1000 genomes]
rs28605633	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28613360	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28618215	1.00[ASN][1000 genomes]
rs28638475	1.00[ASN][1000 genomes]
rs28649737	0.93[ASN][1000 genomes]
rs28650960	0.93[ASN][1000 genomes]
rs28655190	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28660682	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28661501	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28663524	0.87[ASN][1000 genomes]
rs28669685	1.00[ASN][1000 genomes]
rs28682547	0.87[ASN][1000 genomes]
rs28697879	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28729511	0.87[ASN][1000 genomes]
rs28735959	1.00[ASN][1000 genomes]
rs4499185	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4774620	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs4774621	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs4776042	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987194	1.00[ASN][1000 genomes]
rs57864537	0.93[ASN][1000 genomes]
rs58029714	0.93[ASN][1000 genomes]
rs58812575	1.00[ASN][1000 genomes]
rs7163569	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163778	1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164722	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7166034	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7167181	0.93[ASN][1000 genomes]
rs7167680	0.93[ASN][1000 genomes]
rs7167890	0.88[ASN][1000 genomes]
rs7167916	1.00[ASN][1000 genomes]
rs7168076	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7169104	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7169346	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs7170622	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7178069	1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7179156	1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7182148	0.88[ASN][1000 genomes]
rs73408408	0.93[ASN][1000 genomes]
rs73410715	1.00[ASN][1000 genomes]
rs73410759	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7342673	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs744501	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs8023623	1.00[ASN][1000 genomes]
rs8024412	1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8024624	0.93[ASN][1000 genomes]
rs8027637	0.93[ASN][1000 genomes]
rs8030307	1.00[EUR][1000 genomes]
rs8035199	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs8041819	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs8042235	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8042245	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs876549	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9744852	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9920195	0.87[ASN][1000 genomes]
rs9920749	1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[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	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
2	chr15:52647400-52690600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:52663200-52711400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:52663400-52708600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr15:52665200-52720600	Weak transcription	Pancreas	Pancrea
6	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
7	chr15:52669400-52693400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:52674000-52703800	Weak transcription	Fetal Brain Male	brain
10	chr15:52675000-52697400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr15:52676000-52705600	Weak transcription	Fetal Stomach	stomach
12	chr15:52676200-52696800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:52676200-52701800	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:52676400-52696800	Weak transcription	Brain Germinal Matrix	brain
15	chr15:52676400-52696800	Weak transcription	Dnd41	blood
16	chr15:52676400-52697000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:52676400-52699600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:52676400-52701000	Weak transcription	HMEC	breast
19	chr15:52676400-52709800	Weak transcription	NHLF	lung
20	chr15:52676400-52721400	Weak transcription	Gastric	stomach
21	chr15:52676600-52698000	Weak transcription	Fetal Thymus	thymus
22	chr15:52676600-52701800	Weak transcription	Right Ventricle	heart
23	chr15:52676600-52706400	Weak transcription	Lung	lung
24	chr15:52676600-52718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:52677000-52730000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:52679800-52729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
28	chr15:52680600-52719800	Weak transcription	NH-A	brain
29	chr15:52680800-52716400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:52680800-52730000	Weak transcription	Brain Angular Gyrus	brain
31	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
32	chr15:52681000-52696600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:52681000-52696800	Weak transcription	Ovary	ovary
34	chr15:52681000-52706800	Weak transcription	Brain Substantia Nigra	brain
35	chr15:52681200-52701000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr15:52682600-52693200	Strong transcription	Primary B cells from cord blood	blood
37	chr15:52683000-52690400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr15:52683800-52696800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:52684000-52693600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:52684000-52719800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:52684400-52696600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:52684400-52696800	Weak transcription	HSMM	muscle
43	chr15:52684600-52695400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:52684800-52695600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:52684800-52701000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:52684800-52719800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr15:52684800-52730000	Weak transcription	Brain Hippocampus Middle	brain
48	chr15:52685000-52690000	Weak transcription	Osteobl	bone
49	chr15:52685000-52696800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:52685000-52701200	Weak transcription	A549	lung

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