Variant report

Variant	rs875462
Chromosome Location	chr6:15538436-15538437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11756738	0.94[CEU][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13192791	0.90[EUR][1000 genomes]
rs13198195	0.82[EUR][1000 genomes]
rs13198335	0.83[EUR][1000 genomes]
rs13212086	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs13217513	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1988856	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2056942	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619531	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2619551	0.82[EUR][1000 genomes]
rs6903266	0.93[CEU][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6906100	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6918834	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6937379	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71533648	0.91[EUR][1000 genomes]
rs760665	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs760666	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7738263	0.90[EUR][1000 genomes]
rs7745876	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7745907	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7758659	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7760564	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7765924	0.92[EUR][1000 genomes]
rs7768128	0.83[EUR][1000 genomes]
rs9296983	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9296986	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9383063	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9396593	0.87[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9464796	1.00[CEU][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv522265	chr6:15494177-15546213	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv428473	chr6:15522653-15595739	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs875462	DEK	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15523600-15540000	Weak transcription	NHEK	skin
2	chr6:15524400-15549400	Weak transcription	Hela-S3	cervix
3	chr6:15524800-15549800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:15525000-15539000	Weak transcription	Brain Angular Gyrus	brain
5	chr6:15525000-15553400	Weak transcription	Ovary	ovary
6	chr6:15525400-15539000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:15527200-15541400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:15528400-15547400	Weak transcription	Fetal Kidney	kidney
9	chr6:15528600-15543600	Weak transcription	GM12878-XiMat	blood
10	chr6:15528600-15546800	Weak transcription	Fetal Lung	lung
11	chr6:15529000-15541200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:15529400-15549800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:15530000-15538800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:15531800-15545800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:15532600-15549800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:15532800-15539000	Weak transcription	Brain Anterior Caudate	brain
17	chr6:15532800-15542000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:15532800-15544200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:15533600-15551000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr6:15533800-15539600	Weak transcription	Esophagus	oesophagus
21	chr6:15533800-15542400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:15534000-15544000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:15534000-15551600	Weak transcription	Aorta	Aorta
24	chr6:15534400-15539000	Weak transcription	Gastric	stomach
25	chr6:15534400-15539800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:15534400-15539800	Weak transcription	Primary B cells from cord blood	blood
27	chr6:15534400-15544000	Weak transcription	Primary T cells from cord blood	blood
28	chr6:15534400-15544600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:15534400-15551000	Weak transcription	K562	blood
30	chr6:15534400-15609800	Weak transcription	Thymus	Thymus
31	chr6:15535800-15543400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr6:15536000-15544000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:15536200-15538600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:15536600-15538800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:15536600-15539200	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:15536800-15539600	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:15536800-15541200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:15537000-15539000	Weak transcription	Fetal Heart	heart
39	chr6:15537000-15539000	Weak transcription	Lung	lung
40	chr6:15537000-15539400	Weak transcription	Spleen	Spleen
41	chr6:15537000-15539800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr6:15537000-15544600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:15537000-15549800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:15537000-15550000	Weak transcription	Psoas Muscle	Psoas
45	chr6:15537000-15551000	Weak transcription	Left Ventricle	heart
46	chr6:15537000-15551600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr6:15537000-15551800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:15537000-15554400	Weak transcription	Fetal Intestine Large	intestine
49	chr6:15537200-15538600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:15537200-15546000	Weak transcription	Right Atrium	heart

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