Variant report

Variant	rs8024901
Chromosome Location	chr15:57574308-57574309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10467927	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10467928	0.91[JPT][hapmap]
rs10467929	0.91[JPT][hapmap]
rs11071308	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs11853810	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11856210	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12904634	0.84[MKK][hapmap]
rs13379847	0.90[JPT][hapmap]
rs1545728	0.88[MKK][hapmap];0.90[YRI][hapmap]
rs16977270	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs16977278	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16977306	0.82[CEU][hapmap]
rs16977374	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867638	1.00[YRI][hapmap]
rs2169467	0.91[JPT][hapmap]
rs2290938	0.88[MKK][hapmap]
rs2414493	0.85[JPT][hapmap]
rs2591062	1.00[YRI][hapmap]
rs2591066	1.00[YRI][hapmap]
rs2591068	0.88[CEU][hapmap]
rs2593211	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2593216	0.80[YRI][hapmap]
rs2593228	0.90[YRI][hapmap]
rs2593249	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2593252	0.89[JPT][hapmap]
rs2615220	0.90[YRI][hapmap]
rs2615226	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2615227	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2615228	1.00[YRI][hapmap]
rs2703593	0.82[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs2703595	0.88[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs2703600	1.00[YRI][hapmap]
rs2703614	0.91[JPT][hapmap]
rs2703619	0.80[YRI][hapmap]
rs2733309	1.00[YRI][hapmap]
rs2733310	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs2733320	1.00[YRI][hapmap]
rs2733323	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2733330	1.00[YRI][hapmap]
rs2733333	0.91[JPT][hapmap]
rs2733334	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs28445470	0.95[ASN][1000 genomes]
rs28653088	0.94[ASN][1000 genomes]
rs3095821	0.91[MKK][hapmap];0.90[YRI][hapmap]
rs3794613	0.88[MKK][hapmap]
rs3803453	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs4774915	0.95[ASN][1000 genomes]
rs4774916	0.95[ASN][1000 genomes]
rs4774921	0.81[ASN][1000 genomes]
rs6493907	0.92[ASN][1000 genomes]
rs7163267	0.91[JPT][hapmap]
rs7164298	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.97[ASN][1000 genomes]
rs7164914	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7173477	0.95[ASN][1000 genomes]
rs7173748	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7179311	0.87[CEU][hapmap]
rs7180558	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]
rs7181399	0.82[CEU][hapmap]
rs7182038	0.91[YRI][hapmap]
rs720290	0.81[JPT][hapmap]
rs8026702	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8034502	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8034744	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs8034843	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.97[ASN][1000 genomes]
rs8035916	0.89[JPT][hapmap]
rs8037956	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8039176	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs935326	0.84[MKK][hapmap]
rs9672676	0.80[TSI][hapmap]
rs9806170	0.81[JPT][hapmap]
rs9806199	0.91[JPT][hapmap]
rs997683	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[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	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	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
4	nsv526342	chr15:57565859-57597280	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8024901	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
3	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
4	chr15:57539400-57574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:57544600-57574800	Weak transcription	Fetal Brain Male	brain
6	chr15:57546000-57580600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:57548200-57578000	Weak transcription	Fetal Heart	heart
8	chr15:57552200-57588600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:57552400-57578600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:57553200-57585000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:57556200-57580600	Weak transcription	Stomach Mucosa	stomach
12	chr15:57557000-57584600	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:57557600-57578000	Weak transcription	Pancreas	Pancrea
14	chr15:57557600-57588600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:57562600-57575600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:57562600-57578000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:57562600-57584200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr15:57562600-57584600	Strong transcription	Fetal Muscle Leg	muscle
19	chr15:57564000-57582400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:57564000-57583600	Strong transcription	Dnd41	blood
21	chr15:57564800-57575600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:57564800-57584600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:57565000-57576400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:57565000-57583400	Strong transcription	Thymus	Thymus
25	chr15:57565200-57574600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:57565200-57575200	Strong transcription	Fetal Lung	lung
27	chr15:57565600-57584600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:57565800-57578000	Weak transcription	Right Ventricle	heart
29	chr15:57566000-57574400	Weak transcription	Brain Anterior Caudate	brain
30	chr15:57566000-57577800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:57566000-57577800	Weak transcription	Brain Substantia Nigra	brain
32	chr15:57566000-57579000	Weak transcription	Brain Germinal Matrix	brain
33	chr15:57566000-57584400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr15:57566000-57591600	Weak transcription	Esophagus	oesophagus
35	chr15:57566200-57578400	Weak transcription	Spleen	Spleen
36	chr15:57566400-57577800	Weak transcription	Small Intestine	intestine
37	chr15:57566400-57578000	Weak transcription	Ovary	ovary
38	chr15:57567000-57574800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:57567000-57579000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr15:57567400-57575800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:57567400-57577600	Weak transcription	A549	lung
42	chr15:57567800-57578600	Weak transcription	NHEK	skin
43	chr15:57568000-57576000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr15:57568000-57578200	Weak transcription	Brain Angular Gyrus	brain
45	chr15:57568000-57578400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr15:57568000-57582600	Weak transcription	Aorta	Aorta
47	chr15:57568000-57588400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:57568000-57590600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:57568200-57574800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:57568200-57577800	Weak transcription	Gastric	stomach

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