Variant report

Variant	rs9470885
Chromosome Location	chr6:38445399-38445400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12191714	1.00[JPT][hapmap]
rs12206324	1.00[JPT][hapmap]
rs12206905	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12212983	1.00[JPT][hapmap]
rs12215850	1.00[JPT][hapmap]
rs1883610	0.86[JPT][hapmap]
rs1983605	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs28445226	1.00[JPT][hapmap]
rs4236058	1.00[JPT][hapmap]
rs4711542	1.00[JPT][hapmap]
rs4711546	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4714152	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4714157	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4714161	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4714165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60936387	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61192259	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6458054	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6899746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6901086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6904723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6909898	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6933268	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6933758	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6940319	1.00[JPT][hapmap]
rs742515	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7748599	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7749685	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7759629	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7766214	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7770868	0.88[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs871183	1.00[JPT][hapmap]
rs9349073	1.00[JPT][hapmap]
rs9357272	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9380743	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9394495	1.00[JPT][hapmap]
rs9470888	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9470891	0.88[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1030889	chr6:38374812-38450432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9470885	C6orf106	cis	cerebellum	SCAN
rs9470885	GLO1	cis	cerebellum	SCAN
rs9470885	BYSL	cis	parietal	SCAN
rs9470885	GLO1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38396400-38449800	Weak transcription	Primary B cells from cord blood	blood
2	chr6:38412200-38445600	Weak transcription	Primary T cells from cord blood	blood
3	chr6:38437000-38455400	Weak transcription	Gastric	stomach
4	chr6:38440200-38449800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:38443200-38445400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:38443200-38445600	Enhancers	Brain Germinal Matrix	brain
7	chr6:38443400-38447400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr6:38443600-38446000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:38443600-38446200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:38443600-38446600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:38444200-38446800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr6:38444200-38447000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:38444400-38447200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:38444600-38447400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:38444800-38446000	Enhancers	Fetal Brain Male	brain
17	chr6:38444800-38446200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr6:38444800-38446600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:38444800-38447000	Enhancers	H9 Cell Line	embryonic stem cell
20	chr6:38444800-38447200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:38444800-38449800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:38445000-38445800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr6:38445000-38448600	Weak transcription	Fetal Brain Female	brain
24	chr6:38445200-38446200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:38445200-38446200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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