Variant report

Variant	rs10454039
Chromosome Location	chr15:42832534-42832535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42831892..42833394-chr15:42842202..42844793,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1060291	0.90[CEU][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs10851410	0.95[CEU][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs10851411	0.89[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11022	0.95[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs11070374	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11631193	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11636577	0.80[CEU][hapmap]
rs11638208	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1197547	0.84[MKK][hapmap]
rs12102055	1.00[YRI][hapmap]
rs12324113	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12324717	0.95[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs12594483	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs12594855	1.00[YRI][hapmap]
rs12903432	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906497	1.00[YRI][hapmap]
rs12906697	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12913324	0.82[EUR][1000 genomes]
rs12917018	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs12917189	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs16957091	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs1900921	0.95[CEU][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs1995939	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs2241827	1.00[YRI][hapmap]
rs2241998	0.89[ASW][hapmap];0.95[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2255995	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280048	1.00[YRI][hapmap]
rs2412711	1.00[YRI][hapmap]
rs2412741	1.00[YRI][hapmap]
rs2595939	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2595940	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2595941	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2617236	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2617238	0.82[JPT][hapmap]
rs28886308	0.83[EUR][1000 genomes]
rs2899051	0.85[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs2899057	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3115883	1.00[YRI][hapmap]
rs3199486	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs34643746	0.94[EUR][1000 genomes]
rs3742987	1.00[YRI][hapmap]
rs3742988	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs3986280	0.95[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs4573906	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923947	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs4923948	0.95[CEU][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs4924684	0.90[EUR][1000 genomes]
rs4924690	1.00[YRI][hapmap]
rs4994112	0.88[ASW][hapmap]
rs56357092	0.90[EUR][1000 genomes]
rs60380503	0.87[EUR][1000 genomes]
rs6493060	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs6493061	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs7166373	1.00[YRI][hapmap]
rs7168835	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7169009	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs7169202	1.00[YRI][hapmap]
rs7174041	1.00[YRI][hapmap]
rs731984	0.88[ASW][hapmap]
rs8027427	1.00[YRI][hapmap]
rs8030587	0.88[ASW][hapmap]
rs8033412	0.95[CEU][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs8034447	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs8043472	0.88[ASW][hapmap];1.00[YRI][hapmap]
rs9302112	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9783683	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10454039	TMCO5A	cis	parietal	SCAN
rs10454039	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx
rs10454039	MAP1A	cis	parietal	SCAN
rs10454039	RINT1	trans	cerebellum	SCAN
rs10454039	INO80	cis	parietal	SCAN
rs10454039	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs10454039	MAP1A	cis	cerebellum	SCAN
rs10454039	SNAP23	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42793000-42835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:42793800-42837200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:42797400-42839800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:42797600-42839400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:42799200-42839400	Weak transcription	Stomach Mucosa	stomach
6	chr15:42802400-42839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:42803200-42837200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:42803600-42839400	Weak transcription	A549	lung
9	chr15:42804600-42836400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:42804800-42836400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr15:42804800-42836400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr15:42805400-42836800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:42806200-42836400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:42806200-42839000	Weak transcription	Fetal Brain Male	brain
15	chr15:42808400-42839000	Weak transcription	Fetal Heart	heart
16	chr15:42808800-42836000	Weak transcription	Esophagus	oesophagus
17	chr15:42810200-42840200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:42811000-42837600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:42811800-42836000	Weak transcription	Colonic Mucosa	Colon
20	chr15:42815800-42833000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:42817400-42840200	Weak transcription	Pancreas	Pancrea
22	chr15:42821200-42836200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:42821200-42839800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:42822000-42832800	Strong transcription	Fetal Brain Female	brain
25	chr15:42822200-42840200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:42822800-42840000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:42823000-42835600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:42823400-42840200	Weak transcription	Psoas Muscle	Psoas
29	chr15:42823800-42835600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr15:42823800-42835600	Weak transcription	NHLF	lung
31	chr15:42823800-42838000	Weak transcription	Brain Angular Gyrus	brain
32	chr15:42824000-42834200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:42824000-42835000	Weak transcription	Spleen	Spleen
34	chr15:42824000-42840200	Weak transcription	Small Intestine	intestine
35	chr15:42824200-42835800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:42824200-42835800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:42824200-42835800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:42824400-42839400	Weak transcription	Brain Substantia Nigra	brain
39	chr15:42824600-42834800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:42824600-42835600	Weak transcription	Osteobl	bone
41	chr15:42824600-42836000	Weak transcription	Ovary	ovary
42	chr15:42824600-42836600	Weak transcription	Aorta	Aorta
43	chr15:42824600-42838400	Weak transcription	HepG2	liver
44	chr15:42824600-42839600	Weak transcription	Right Ventricle	heart
45	chr15:42824800-42834800	Weak transcription	GM12878-XiMat	blood
46	chr15:42824800-42835400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr15:42825000-42835600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr15:42825600-42834800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr15:42825600-42834800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr15:42825600-42835800	Weak transcription	NH-A	brain

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