Variant report

Variant	rs10515453
Chromosome Location	chr5:112326951-112326952
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112312686..112316155-chr5:112325860..112328052,3	K562	blood:
2	chr5:112325917..112328748-chr5:112331994..112335756,3	K562	blood:
3	chr5:112313991..112316155-chr5:112326453..112328052,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10059132	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10076751	0.81[EUR][1000 genomes]
rs10463645	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13360862	0.84[MEX][hapmap]
rs1422222	0.95[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1978430	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2080898	1.00[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs2080899	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3209874	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3733968	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs4309965	0.81[ASW][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap]
rs58280144	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6594654	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6594655	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6865320	0.81[CHB][hapmap]
rs6876686	0.91[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6888851	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6888965	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6892784	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7033	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7733267	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9326868	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10515453	TSLP	cis	parietal	SCAN
rs10515453	MCC	cis	cerebellum	SCAN
rs10515453	DCP2	cis	parietal	SCAN
rs10515453	AQPEP	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112313200-112329000	Weak transcription	Spleen	Spleen
2	chr5:112313800-112337600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:112314000-112329000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:112314000-112335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:112314000-112337200	Weak transcription	Lung	lung
6	chr5:112314000-112338200	Weak transcription	Gastric	stomach
7	chr5:112314200-112328800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:112314200-112328800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:112314200-112332000	Weak transcription	Fetal Kidney	kidney
10	chr5:112314200-112332000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:112314200-112337000	Weak transcription	HSMMtube	muscle
12	chr5:112314200-112338200	Weak transcription	Aorta	Aorta
13	chr5:112314200-112341000	Weak transcription	Small Intestine	intestine
14	chr5:112314200-112349600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
16	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
17	chr5:112314400-112338400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:112314800-112332000	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:112314800-112332000	Weak transcription	NHLF	lung
20	chr5:112314800-112332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:112314800-112337200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:112314800-112349200	Weak transcription	Brain Substantia Nigra	brain
23	chr5:112315400-112330800	Weak transcription	Brain Anterior Caudate	brain
24	chr5:112315600-112328600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:112315600-112332000	Weak transcription	NHDF-Ad	bronchial
26	chr5:112315600-112332200	Weak transcription	Ovary	ovary
27	chr5:112315600-112339400	Weak transcription	Hela-S3	cervix
28	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
29	chr5:112315800-112329200	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:112315800-112334600	Weak transcription	Brain Germinal Matrix	brain
31	chr5:112316000-112332200	Weak transcription	Fetal Brain Female	brain
32	chr5:112316000-112337000	Weak transcription	A549	lung
33	chr5:112316400-112330000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr5:112316600-112330000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:112317000-112332000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr5:112317000-112338200	Weak transcription	Left Ventricle	heart
37	chr5:112317800-112328400	Weak transcription	Osteobl	bone
38	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr5:112318000-112329600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:112318000-112336400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr5:112318400-112329000	Weak transcription	NHEK	skin
42	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:112318600-112328400	Weak transcription	NH-A	brain
44	chr5:112319000-112332000	Weak transcription	HMEC	breast
45	chr5:112319000-112335800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:112319200-112328800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:112319400-112328200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:112319400-112336800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:112319800-112330200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:112319800-112332000	Weak transcription	Fetal Brain Male	brain

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