Variant report

Variant	rs4573906
Chromosome Location	chr15:42805000-42805001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10454039	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1060291	0.95[EUR][1000 genomes]
rs10851410	0.88[EUR][1000 genomes]
rs10851411	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11022	0.95[EUR][1000 genomes]
rs11070374	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631193	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11636577	0.84[EUR][1000 genomes]
rs11638208	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12324113	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12324717	0.89[EUR][1000 genomes]
rs12898937	0.82[EUR][1000 genomes]
rs12903432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906697	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12913324	0.87[EUR][1000 genomes]
rs1900920	0.83[EUR][1000 genomes]
rs1900921	0.95[EUR][1000 genomes]
rs2241998	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2255995	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412715	0.81[EUR][1000 genomes]
rs2595939	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595940	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595941	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617235	0.82[EUR][1000 genomes]
rs2617236	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2617237	0.82[EUR][1000 genomes]
rs28886308	0.88[EUR][1000 genomes]
rs2899051	0.91[EUR][1000 genomes]
rs2899057	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34643746	0.89[EUR][1000 genomes]
rs3986280	0.89[EUR][1000 genomes]
rs4923947	0.98[ASN][1000 genomes]
rs4923948	0.95[EUR][1000 genomes]
rs4924678	0.81[EUR][1000 genomes]
rs4924684	0.95[EUR][1000 genomes]
rs56357092	0.95[EUR][1000 genomes]
rs60380503	0.92[EUR][1000 genomes]
rs7168835	0.82[AMR][1000 genomes]
rs7169615	0.84[EUR][1000 genomes]
rs8033412	0.95[EUR][1000 genomes]
rs8034232	0.83[EUR][1000 genomes]
rs8034238	0.82[EUR][1000 genomes]
rs9302112	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4573906	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx
rs4573906	CEP27	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:129 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42788400-42808000	Weak transcription	Esophagus	oesophagus
2	chr15:42788600-42805600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:42788600-42806600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:42788600-42807200	Weak transcription	Fetal Kidney	kidney
5	chr15:42788800-42805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:42788800-42805400	Weak transcription	Brain Germinal Matrix	brain
7	chr15:42789000-42805400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:42789000-42806400	Weak transcription	Thymus	Thymus
9	chr15:42789200-42805800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:42789200-42806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:42790600-42805200	Weak transcription	Dnd41	blood
12	chr15:42790600-42806600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:42790600-42807200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:42790800-42805000	Weak transcription	Fetal Thymus	thymus
15	chr15:42790800-42809800	Weak transcription	Spleen	Spleen
16	chr15:42790800-42810000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:42790800-42821400	Weak transcription	Right Ventricle	heart
18	chr15:42791200-42809800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:42792200-42805800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:42792400-42805400	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:42792400-42806600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:42792400-42807400	Weak transcription	HMEC	breast
23	chr15:42792600-42805600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:42793000-42809800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:42793000-42835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:42793600-42805400	Weak transcription	Liver	Liver
27	chr15:42793600-42807400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:42793800-42806400	Weak transcription	Pancreas	Pancrea
29	chr15:42793800-42837200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:42797400-42839800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:42797600-42805000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:42797600-42805200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:42797600-42805400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr15:42797600-42805400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:42797600-42807000	Weak transcription	Colonic Mucosa	Colon
36	chr15:42797600-42822200	Weak transcription	Small Intestine	intestine
37	chr15:42797600-42839400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:42797800-42805200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:42797800-42805400	Weak transcription	HepG2	liver
40	chr15:42797800-42806600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr15:42798600-42808400	Weak transcription	Gastric	stomach
42	chr15:42799200-42805000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:42799200-42839400	Weak transcription	Stomach Mucosa	stomach
44	chr15:42800400-42805400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:42800400-42807200	Weak transcription	GM12878-XiMat	blood
46	chr15:42800800-42805400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr15:42800800-42806400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:42800800-42806400	Weak transcription	Lung	lung
49	chr15:42801000-42809400	Weak transcription	Fetal Lung	lung
50	chr15:42801200-42807800	Weak transcription	Fetal Heart	heart

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