Variant report

Variant	rs2394450
Chromosome Location	chr6:30817501-30817502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr6:30817483-30818055	SK-N-SH	brain:	n/a	n/a
2	TCF7L2	chr6:30817330-30817797	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30816135..30818662-chr6:30876790..30878789,2	K562	blood:
2	chr6:30814424..30817937-chr6:30849019..30852528,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237923	TF binding region
ENSG00000213780	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs2394449	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2394451	0.87[ASN][1000 genomes]
rs2517582	0.83[ASN][1000 genomes]
rs2535338	0.85[ASN][1000 genomes]
rs3094109	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3094720	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3095342	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3095343	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3095344	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3095346	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3095348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095349	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3095350	0.83[EUR][1000 genomes]
rs3095351	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3095352	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3095354	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129990	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129993	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130647	0.84[EUR][1000 genomes]
rs3130649	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130650	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130651	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130652	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130653	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130655	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130656	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130786	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130787	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130789	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130791	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130792	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130793	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130794	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130795	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130796	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131027	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131030	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3131031	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131033	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3131066	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3132573	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3132574	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3132575	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3132576	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3132578	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9262251	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2394450	VARSL	cis	multi-tissue	Pritchard
rs2394450	HIST1H2AL	cis	cerebellum	SCAN
rs2394450	HCG22	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30812400-30822600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:30812600-30820600	Weak transcription	Right Atrium	heart
3	chr6:30814800-30817600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:30816200-30822200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:30816200-30824600	Weak transcription	Fetal Kidney	kidney
6	chr6:30816600-30817600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:30816600-30817600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:30816600-30817800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr6:30816600-30818000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:30816600-30819400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:30817000-30817800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:30817200-30817600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:30817200-30818000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:30817200-30818000	Enhancers	Fetal Lung	lung
15	chr6:30817400-30818000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
16	chr6:30817400-30820600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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