Variant report

Variant	rs9469693
Chromosome Location	chr6:34013250-34013251
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	chr6:34012736..34015339-chr6:34023792..34026644,2	K562	blood:
2	chr6:34011747..34013677-chr6:34019752..34021828,2	K562	blood:

Variant related genes	Relation type
ENSG00000124493	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12663035	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12664932	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1565365	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1565366	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1873254	0.82[ASW][hapmap];0.93[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2228623	0.84[ASN][1000 genomes]
rs3734361	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711374	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713735	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922166	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7772059	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7775780	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366836	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366837	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9368789	0.84[ASN][1000 genomes]
rs9368791	0.94[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9461949	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469690	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469691	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469697	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv916210	chr6:33804111-34144062	Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv462900	chr6:33932442-34195011	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv602843	chr6:33932442-34195011	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv462901	chr6:33953646-34050917	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv602861	chr6:33953646-34050917	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	esv3436593	chr6:34010074-34014572	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9469693	GRM4	cis	cerebellum	SCAN
rs9469693	NUDT3	cis	parietal	SCAN
rs9469693	TMEM217	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33984400-34023000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:33988000-34013600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:34000200-34016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:34002800-34027000	Weak transcription	Spleen	Spleen
5	chr6:34004000-34013400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:34004200-34013400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:34004400-34013400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:34010400-34013400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:34011600-34013600	Weak transcription	Brain Anterior Caudate	brain
10	chr6:34012400-34013600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr6:34012600-34013400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:34012600-34013400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:34012600-34013600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr6:34012600-34013600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr6:34012600-34014400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:34013000-34013400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:34013000-34013400	Enhancers	Brain Germinal Matrix	brain
18	chr6:34013000-34013800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:34013000-34014000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr6:34013000-34014600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:34013200-34013600	Weak transcription	Fetal Brain Male	brain

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