Variant report

Variant	rs2448810
Chromosome Location	chr15:52083357-52083358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1133878	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964482	1.00[ASN][1000 genomes]
rs16964483	1.00[ASN][1000 genomes]
rs17611465	1.00[ASN][1000 genomes]
rs1863429	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1972419	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016057	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124587	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448945	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2554354	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554355	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570230	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570243	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593169	1.00[ASN][1000 genomes]
rs2593184	0.81[AMR][1000 genomes]
rs2606128	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2606130	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606133	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622765	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622778	1.00[ASN][1000 genomes]
rs2623245	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623247	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623251	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623258	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623263	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623270	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652595	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652597	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28522862	1.00[ASN][1000 genomes]
rs28654101	1.00[ASN][1000 genomes]
rs28876142	1.00[ASN][1000 genomes]
rs691738	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71472920	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv3411789	chr15:52052789-52087519	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2448810	RP11-707P17.1	cis	Nerve Tibial	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
2	chr15:52052600-52106600	Weak transcription	HSMM	muscle
3	chr15:52053400-52090600	Weak transcription	Pancreas	Pancrea
4	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:52060400-52085400	Weak transcription	Fetal Lung	lung
6	chr15:52060600-52087400	Weak transcription	Gastric	stomach
7	chr15:52060600-52088400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:52060600-52091000	Weak transcription	Right Ventricle	heart
9	chr15:52060800-52101200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr15:52060800-52102600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:52060800-52105400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr15:52061600-52085400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:52061600-52112000	Weak transcription	NHLF	lung
14	chr15:52061800-52098600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:52064400-52090400	Weak transcription	Left Ventricle	heart
16	chr15:52065600-52090600	Weak transcription	Spleen	Spleen
17	chr15:52065800-52091000	Weak transcription	Esophagus	oesophagus
18	chr15:52067200-52090600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:52067600-52090600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:52067800-52089000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:52069200-52091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:52069400-52085200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:52073400-52085400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:52074000-52090600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:52074000-52100000	Weak transcription	NHDF-Ad	bronchial
26	chr15:52074800-52102800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:52075000-52088600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:52075000-52090600	Weak transcription	Dnd41	blood
29	chr15:52075600-52089000	Weak transcription	Aorta	Aorta
30	chr15:52076400-52098400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:52076600-52090400	Weak transcription	Primary B cells from cord blood	blood
32	chr15:52076600-52090400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:52076600-52090400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:52076600-52090400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr15:52076600-52090600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr15:52076600-52090600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:52076800-52085400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:52076800-52085600	Weak transcription	Brain Substantia Nigra	brain
39	chr15:52076800-52090800	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:52076800-52090800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr15:52076800-52104400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr15:52077000-52090400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:52077200-52098600	Weak transcription	Fetal Brain Male	brain
44	chr15:52079000-52098400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:52079200-52089600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:52079200-52090600	Weak transcription	Fetal Thymus	thymus
47	chr15:52079200-52098600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:52079400-52089000	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:52079400-52090600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:52079600-52086200	Weak transcription	Brain Cingulate Gyrus	brain

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