Variant report

Variant	rs12898644
Chromosome Location	chr15:52905233-52905234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1080731	1.00[CHB][hapmap]
rs10851521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070908	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070909	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11633933	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11853917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11855616	0.90[CHB][hapmap]
rs11857150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11858743	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12232257	0.92[JPT][hapmap]
rs12902679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12914047	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12915981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13329393	0.90[CHB][hapmap]
rs17614559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1863512	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2288271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs2414160	0.90[CHB][hapmap]
rs2414161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs2414163	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2414167	1.00[CHB][hapmap]
rs34431049	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4390542	1.00[CHB][hapmap]
rs4548810	0.95[CEU][hapmap];0.89[CHB][hapmap]
rs4774634	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4774636	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4776058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4776063	0.90[CHB][hapmap]
rs4776065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4776066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4776068	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62023352	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7167494	0.90[CHB][hapmap]
rs8026800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8030141	0.89[CHB][hapmap]
rs933860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12898644	KIAA1370	cis	uninvolved skin	skin_eQTL
rs12898644	KIAA1370	cis	Lymphoblastoid	GTEx
rs12898644	KIAA1370	cis	normal skin	skin_eQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52861200-52925200	Weak transcription	Stomach Mucosa	stomach
2	chr15:52861800-52908400	Weak transcription	Gastric	stomach
3	chr15:52861800-52934800	Weak transcription	Right Ventricle	heart
4	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
5	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:52872200-52933800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:52872600-52920800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:52873400-52928000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:52873800-52909600	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr15:52874200-52917000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:52875400-52916200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:52878200-52909600	Strong transcription	Liver	Liver
14	chr15:52882200-52920000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:52882400-52906200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr15:52882400-52926000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr15:52885600-52945200	Weak transcription	Spleen	Spleen
18	chr15:52890600-52906000	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr15:52891400-52927600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:52891600-52908400	Weak transcription	Aorta	Aorta
21	chr15:52894600-52906000	Strong transcription	Fetal Intestine Large	intestine
22	chr15:52899000-52920400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:52899400-52906000	Strong transcription	Fetal Thymus	thymus
24	chr15:52899400-52906200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr15:52899600-52906000	Strong transcription	Left Ventricle	heart
26	chr15:52899600-52917000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:52899600-52944400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:52900200-52906400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:52900400-52909600	Strong transcription	Adipose Nuclei	Adipose
30	chr15:52900400-52911800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr15:52900600-52907800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:52900600-52909600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr15:52900600-52944000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr15:52900800-52906000	Strong transcription	Brain Substantia Nigra	brain
35	chr15:52900800-52906200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:52900800-52945200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:52901000-52906000	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:52901000-52906200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr15:52901200-52906000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:52901200-52906200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:52901200-52906800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:52901200-52907400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:52901400-52906200	Strong transcription	Ovary	ovary
44	chr15:52901400-52906200	Strong transcription	HSMMtube	muscle
45	chr15:52901400-52907000	Strong transcription	Thymus	Thymus
46	chr15:52901600-52906000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:52901600-52906000	Strong transcription	Fetal Muscle Leg	muscle
48	chr15:52902200-52943800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:52902400-52905400	Weak transcription	Fetal Brain Female	brain
50	chr15:52902400-52908000	Weak transcription	Psoas Muscle	Psoas

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