Variant report

Variant	rs228186
Chromosome Location	chr6:38317686-38317687
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38294680..38296674-chr6:38317657..38319698,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1033480	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1205108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12191714	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs12201631	0.85[EUR][1000 genomes]
rs12202804	0.84[EUR][1000 genomes]
rs12206324	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[YRI][hapmap]
rs12206905	1.00[CHB][hapmap]
rs12208912	0.81[CEU][hapmap]
rs12212983	1.00[CHB][hapmap]
rs12215330	0.85[CEU][hapmap]
rs12215850	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1931758	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2179532	0.89[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs2179533	0.89[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs228179	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs228180	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228188	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395698	0.84[EUR][1000 genomes]
rs2395699	0.84[EUR][1000 genomes]
rs28445226	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4236058	1.00[CHB][hapmap]
rs4714147	0.91[ASN][1000 genomes]
rs4714148	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6922128	0.80[EUR][1000 genomes]
rs7763775	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871183	0.92[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9349072	0.91[ASN][1000 genomes]
rs9349073	0.81[MEX][hapmap]
rs9394495	1.00[CHB][hapmap]
rs9470891	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv602957	chr6:38305770-38395874	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs228186	C6orf64	cis	cerebellum	SCAN
rs228186	TRERF1	cis	cerebellum	SCAN
rs228186	GLO1	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38285000-38327800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:38299800-38317800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:38301600-38324600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr6:38302000-38318200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:38304600-38323000	Weak transcription	Ovary	ovary
6	chr6:38305000-38318000	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:38307600-38318400	Weak transcription	Fetal Intestine Small	intestine
8	chr6:38309000-38318800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:38309000-38319000	Weak transcription	Esophagus	oesophagus
10	chr6:38309800-38323400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:38310800-38326000	Weak transcription	Lung	lung
12	chr6:38311400-38319000	Weak transcription	Left Ventricle	heart
13	chr6:38311400-38322000	Weak transcription	Primary B cells from cord blood	blood
14	chr6:38312000-38326600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:38313200-38321400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:38313800-38325800	Weak transcription	Psoas Muscle	Psoas
17	chr6:38313800-38331200	Weak transcription	Primary T cells from cord blood	blood
18	chr6:38314000-38319200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:38314200-38319400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:38314600-38318400	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:38314800-38317800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:38314800-38318000	Weak transcription	HSMM	muscle
23	chr6:38314800-38325800	Weak transcription	Right Atrium	heart
24	chr6:38315000-38317800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:38315000-38318000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:38315000-38318200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:38315200-38318600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:38315200-38325800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:38315800-38339000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:38316200-38318400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:38316400-38317800	Enhancers	GM12878-XiMat	blood
32	chr6:38316400-38318400	Weak transcription	Brain Anterior Caudate	brain
33	chr6:38316400-38318600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:38316400-38318600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:38316600-38318000	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:38316600-38319200	Enhancers	Fetal Stomach	stomach
37	chr6:38316600-38321600	Weak transcription	Fetal Brain Female	brain
38	chr6:38316600-38322400	Weak transcription	Brain Angular Gyrus	brain
39	chr6:38316800-38318600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:38316800-38322800	Weak transcription	Brain Substantia Nigra	brain
41	chr6:38317200-38318000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:38317200-38319200	Enhancers	Osteobl	bone
43	chr6:38317400-38318000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:38317400-38318200	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr6:38317400-38318200	Enhancers	Small Intestine	intestine
46	chr6:38317400-38319200	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr6:38317400-38319200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:38317400-38319200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr6:38317400-38319200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:38317400-38319200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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