Variant report

Variant	rs10851521
Chromosome Location	chr15:52942111-52942112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr15:52941897-52945775	SK-N-SH	brain:	n/a	chr15:52944270-52944284
2	NFIC	chr15:52941782-52942372	ECC-1	luminal epithelium:	n/a	chr15:52942062-52942078 chr15:52942061-52942078

Variant related genes	Relation type
ENSG00000259935	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1080731	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11070907	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070908	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070909	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11633933	0.83[AMR][1000 genomes]
rs11853917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855616	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs11857150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858743	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12232257	0.90[JPT][hapmap]
rs12898644	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]
rs12902679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12914047	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13329393	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs17614559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1863512	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2288271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2414160	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs2414161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2414163	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2414166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2414167	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs34431049	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4390542	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4548810	0.95[CEU][hapmap];0.88[CHB][hapmap]
rs4774634	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4774636	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4776058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4776063	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4776065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4776066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4776068	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62023352	0.83[ASN][1000 genomes]
rs7167494	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs8026800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8030141	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs933860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[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	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	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
4	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
5	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
rs10851521	KIAA1370	cis	normal skin	skin_eQTL
rs10851521	KIAA1370	cis	Lymphoblastoid	GTEx
rs10851521	KIAA1370	cis	uninvolved skin	skin_eQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
2	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:52885600-52945200	Weak transcription	Spleen	Spleen
5	chr15:52899600-52944400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:52900600-52944000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr15:52900800-52945200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:52902200-52943800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:52903400-52943800	Weak transcription	Hela-S3	cervix
10	chr15:52903400-52944000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:52903600-52942400	Weak transcription	Dnd41	blood
12	chr15:52903600-52945400	Weak transcription	Colonic Mucosa	Colon
13	chr15:52904000-52943400	Weak transcription	Fetal Kidney	kidney
14	chr15:52904000-52945400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
16	chr15:52906200-52944000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:52908600-52956200	Weak transcription	Gastric	stomach
18	chr15:52909000-52942400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:52909600-52944000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:52909600-52950800	Weak transcription	Pancreas	Pancrea
21	chr15:52915600-52944200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:52916200-52942800	Weak transcription	Fetal Brain Female	brain
23	chr15:52917000-52943600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:52920800-52942800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr15:52923200-52945200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:52927800-52943800	Weak transcription	Fetal Muscle Leg	muscle
27	chr15:52927800-52947600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:52927800-52958600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:52928000-52942400	Weak transcription	Brain Germinal Matrix	brain
30	chr15:52928000-52944000	Weak transcription	Fetal Intestine Small	intestine
31	chr15:52928000-52955200	Weak transcription	Thymus	Thymus
32	chr15:52928000-52956400	Weak transcription	Lung	lung
33	chr15:52928200-52943800	Weak transcription	Fetal Stomach	stomach
34	chr15:52928200-52945400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:52929200-52942800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:52929400-52945200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:52929800-52944000	Weak transcription	Aorta	Aorta
38	chr15:52929800-52945200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:52930400-52943800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:52930600-52942800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:52931000-52944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:52934400-52943800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:52935000-52943600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr15:52935200-52943000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr15:52935200-52943400	Weak transcription	HSMM	muscle
46	chr15:52935200-52943600	Weak transcription	Right Atrium	heart
47	chr15:52935200-52943800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:52935400-52943200	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:52935400-52943400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:52935400-52943600	Weak transcription	HMEC	breast

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