Variant report

Variant	rs1614699
Chromosome Location	chr6:38738748-38738749
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	chr6:38670515..38672545-chr6:38737534..38740411,2	K562	blood:

Variant related genes	Relation type
ENSG00000124767	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1018437	0.93[JPT][hapmap]
rs1033525	0.81[ASN][1000 genomes]
rs1033526	0.81[ASN][1000 genomes]
rs1157884	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1630487	0.90[ASN][1000 genomes]
rs1678638	0.93[JPT][hapmap]
rs1678657	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1678661	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1678667	0.85[ASN][1000 genomes]
rs1678669	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1678675	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1678717	0.93[JPT][hapmap]
rs1678718	0.93[JPT][hapmap]
rs1678725	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs1678742	0.93[JPT][hapmap]
rs1738177	0.87[JPT][hapmap]
rs1738184	0.93[JPT][hapmap]
rs1738192	0.89[CEU][hapmap];0.93[JPT][hapmap]
rs1738203	0.93[JPT][hapmap]
rs1738231	0.81[JPT][hapmap]
rs1738232	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1738236	0.92[ASN][1000 genomes]
rs1738238	0.87[ASN][1000 genomes]
rs1738239	0.86[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1738240	0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1738241	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1738243	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1738247	0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1738263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2206860	0.87[JPT][hapmap]
rs2395709	0.93[JPT][hapmap]
rs2746170	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap]
rs4286777	0.89[JPT][hapmap]
rs4380739	0.87[JPT][hapmap]
rs4386804	0.93[JPT][hapmap]
rs4391252	0.93[JPT][hapmap]
rs4443498	0.93[JPT][hapmap]
rs4571559	0.93[JPT][hapmap]
rs4590258	0.93[JPT][hapmap]
rs4711558	0.93[JPT][hapmap]
rs4714193	0.93[JPT][hapmap]
rs6458080	0.93[JPT][hapmap]
rs6458081	0.93[JPT][hapmap]
rs6931736	0.93[JPT][hapmap]
rs761348	0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs769064	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap]
rs862422	0.93[JPT][hapmap]
rs862425	0.93[JPT][hapmap]
rs862427	0.89[CEU][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs9296265	0.93[JPT][hapmap]
rs9357290	0.93[JPT][hapmap]
rs9366982	0.93[JPT][hapmap]
rs9369089	0.93[JPT][hapmap]
rs9380789	0.93[JPT][hapmap]
rs9380791	0.81[JPT][hapmap]
rs9380796	0.93[JPT][hapmap]
rs9380798	0.93[JPT][hapmap]
rs9380799	0.93[JPT][hapmap]
rs9394531	0.87[JPT][hapmap]
rs9394547	0.93[JPT][hapmap]
rs9394550	0.93[JPT][hapmap]
rs982705	0.81[CHD][hapmap];0.93[JPT][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	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
2	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv462915	chr6:38728142-38773293	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv602959	chr6:38728142-38786528	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv470814	chr6:38728142-38790149	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1614699	TFEB	cis	parietal	SCAN
rs1614699	GUCA1B	cis	cerebellum	SCAN
rs1614699	CPNE5	cis	cerebellum	SCAN
rs1614699	APOBEC2	cis	cerebellum	SCAN
rs1614699	GNB2	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38736800-38739000	Weak transcription	GM12878-XiMat	blood
2	chr6:38738200-38738800	Enhancers	NHEK	skin
3	chr6:38738200-38739800	Enhancers	HMEC	breast
4	chr6:38738200-38740200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:38738400-38739800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:38738400-38740200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:38738600-38739400	Flanking Active TSS	HUVEC	blood vessel
8	chr6:38738600-38739400	Enhancers	K562	blood

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