Variant report

Variant	rs7180558
Chromosome Location	chr15:57559387-57559388
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10467927	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10467928	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs10467929	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs11071308	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs11853810	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11856210	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11856411	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs13379847	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs16977270	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs16977278	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs16977329	0.96[YRI][hapmap]
rs16977374	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867639	0.96[YRI][hapmap]
rs1867641	0.83[ASW][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap]
rs2169467	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2414493	0.82[CHB][hapmap]
rs2591068	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2593211	0.82[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[MKK][hapmap]
rs2593217	1.00[YRI][hapmap]
rs2593221	1.00[YRI][hapmap]
rs2593235	0.81[AFR][1000 genomes]
rs2593249	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2593252	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2615226	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2615227	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2703593	0.83[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2703594	0.82[EUR][1000 genomes]
rs2703595	0.82[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2703599	1.00[YRI][hapmap]
rs2703614	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2733310	0.83[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs2733316	0.96[YRI][hapmap]
rs2733317	0.96[YRI][hapmap]
rs2733323	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2733333	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2733334	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2733343	0.92[YRI][hapmap]
rs2733345	0.88[YRI][hapmap]
rs28445470	0.99[ASN][1000 genomes]
rs28653088	0.97[ASN][1000 genomes]
rs3803453	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.92[ASN][1000 genomes]
rs4774915	0.99[ASN][1000 genomes]
rs4774916	0.99[ASN][1000 genomes]
rs4774921	0.86[AFR][1000 genomes]
rs6493900	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs6493907	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7163267	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs7164298	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.95[ASN][1000 genomes]
rs7164914	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7173477	0.99[ASN][1000 genomes]
rs7173748	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7179311	0.81[CEU][hapmap]
rs720290	0.84[CHB][hapmap]
rs8024901	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8026702	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs8034502	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8034744	0.83[TSI][hapmap]
rs8034843	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs8035916	0.83[JPT][hapmap]
rs8037956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037987	1.00[YRI][hapmap]
rs8039176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8042322	1.00[YRI][hapmap]
rs8043103	1.00[YRI][hapmap]
rs935329	0.96[YRI][hapmap]
rs9672676	0.83[TSI][hapmap]
rs9806170	0.83[CHB][hapmap]
rs9806199	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs997683	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7180558	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
4	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
5	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
6	chr15:57533600-57568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:57536800-57574200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
9	chr15:57538400-57564800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:57539400-57574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:57539600-57565200	Weak transcription	Aorta	Aorta
12	chr15:57539600-57565200	Weak transcription	Esophagus	oesophagus
13	chr15:57540600-57565400	Weak transcription	Ovary	ovary
14	chr15:57543200-57565200	Weak transcription	Right Ventricle	heart
15	chr15:57544600-57574800	Weak transcription	Fetal Brain Male	brain
16	chr15:57545800-57565200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:57546000-57580600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:57548200-57578000	Weak transcription	Fetal Heart	heart
19	chr15:57550400-57560400	Strong transcription	Dnd41	blood
20	chr15:57552000-57565200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:57552000-57565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:57552200-57560000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:57552200-57565200	Weak transcription	Psoas Muscle	Psoas
24	chr15:57552200-57565200	Weak transcription	Small Intestine	intestine
25	chr15:57552200-57573200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:57552200-57588600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr15:57552400-57565600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr15:57552400-57578600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:57552800-57560200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:57553000-57560800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:57553200-57560400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:57553200-57585000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:57553600-57560800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:57553800-57560400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr15:57553800-57560400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr15:57553800-57561200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:57553800-57563400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:57554000-57560800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:57554000-57560800	Strong transcription	Thymus	Thymus
40	chr15:57554200-57560400	Strong transcription	Fetal Kidney	kidney
41	chr15:57554200-57560800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr15:57554200-57560800	Strong transcription	Fetal Muscle Leg	muscle
43	chr15:57554200-57561000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:57554200-57568800	Strong transcription	Primary T cells from cord blood	blood
45	chr15:57554400-57560400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:57554400-57561000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:57555000-57560200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:57555000-57564200	Weak transcription	Brain Angular Gyrus	brain
49	chr15:57555400-57565400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:57556000-57564800	Weak transcription	A549	lung

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