Variant report

Variant	rs4236060
Chromosome Location	chr6:38470087-38470088
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	chr6:38456452..38459081-chr6:38467880..38470353,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10947738	0.87[EUR][1000 genomes]
rs10947739	1.00[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs13219518	0.86[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs1699003	0.82[ASW][hapmap]
rs1699007	0.82[ASW][hapmap]
rs2814883	0.82[ASW][hapmap]
rs2814894	0.82[ASW][hapmap]
rs3923809	0.90[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4392718	0.82[ASW][hapmap]
rs6920488	0.90[CEU][hapmap]
rs9349077	1.00[YRI][hapmap]
rs9349087	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9349088	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9369057	1.00[YRI][hapmap]
rs9394502	0.82[CEU][hapmap]

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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4236060	KCNK16	cis	cerebellum	SCAN
rs4236060	GLO1	cis	parietal	SCAN
rs4236060	MDFI	cis	parietal	SCAN
rs4236060	FGD2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38451600-38471000	Weak transcription	Psoas Muscle	Psoas
3	chr6:38452400-38496600	Weak transcription	Primary B cells from cord blood	blood
4	chr6:38454400-38486400	Weak transcription	Primary T cells from cord blood	blood
5	chr6:38460800-38473000	Enhancers	Brain Germinal Matrix	brain
6	chr6:38462200-38471200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:38467200-38476400	Weak transcription	Ovary	ovary
8	chr6:38467400-38476400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:38467600-38470600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:38467800-38470600	Weak transcription	Brain Angular Gyrus	brain
11	chr6:38467800-38470800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:38467800-38471800	Weak transcription	Brain Anterior Caudate	brain
13	chr6:38468000-38470600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:38468000-38470600	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:38468000-38472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:38468000-38476400	Weak transcription	Brain Substantia Nigra	brain
17	chr6:38468200-38471800	Weak transcription	Fetal Brain Female	brain
18	chr6:38468200-38472600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:38468600-38471000	Weak transcription	Fetal Brain Male	brain
20	chr6:38468600-38486400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:38469200-38475000	Enhancers	Fetal Muscle Leg	muscle
22	chr6:38469600-38470400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr6:38469600-38470600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:38469800-38470200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:38469800-38472400	Enhancers	HSMMtube	muscle
26	chr6:38469800-38472800	Enhancers	HepG2	liver

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