Variant report

Variant	rs6457009
Chromosome Location	chr6:29676537-29676538
allele	A/G
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	POLR2A	chr6:29673932-29676615	K562	blood:	n/a	n/a
2	TCF12	chr6:29676449-29676710	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:29676395-29677021	GM12878	blood:	n/a	n/a
4	RUNX3	chr6:29676404-29676960	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29673901..29676614-chr6:29690934..29692528,2	MCF-7	breast:

Variant related genes	Relation type
ZDHHC20P1	TF binding region
ENSG00000204642	Chromatin interaction
ENSG00000225864	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1362125	0.85[EUR][1000 genomes]
rs2394661	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2523404	0.84[EUR][1000 genomes]
rs2523405	0.84[EUR][1000 genomes]
rs2735059	0.84[EUR][1000 genomes]
rs2735060	0.84[EUR][1000 genomes]
rs2735062	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4248137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4248138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7762253	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7767671	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9258119	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883530	chr6:29645038-29677641	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv970675	chr6:29657036-29692268	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6457009	ZFP57	cis	lymphoblastoid	seeQTL
rs6457009	TPD52L2	trans	multi-tissue	Pritchard
rs6457009	HLA-F	cis	multi-tissue	Pritchard
rs6457009	NDUFS1	trans	multi-tissue	Pritchard
rs6457009	TFG	trans	multi-tissue	Pritchard
rs6457009	HCG4	cis	multi-tissue	Pritchard
rs6457009	HLA-H	cis	lymphoblastoid	seeQTL
rs6457009	HLA-A	cis	multi-tissue	Pritchard
rs6457009	HLA-A	cis	lymphoblastoid	GTEx
rs6457009	KIT	trans	multi-tissue	Pritchard
rs6457009	HLA-G	cis	multi-tissue	Pritchard
rs6457009	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs6457009	ZSCAN23	cis	parietal	SCAN
rs6457009	HLA-H	cis	multi-tissue	Pritchard
rs6457009	HLA.A29.1	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29664000-29690600	Weak transcription	Right Atrium	heart
2	chr6:29670200-29678200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:29670800-29678200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:29673200-29677000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr6:29673400-29678600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:29673600-29676800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:29674200-29676600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:29674800-29677200	Weak transcription	Spleen	Spleen
9	chr6:29675400-29677800	Flanking Active TSS	Thymus	Thymus
10	chr6:29675800-29676600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr6:29676000-29676600	Enhancers	Primary B cells from peripheral blood	blood
12	chr6:29676000-29676600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:29676000-29676600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr6:29676000-29677400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr6:29676200-29676600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:29676200-29676600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr6:29676200-29676600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:29676200-29676600	Enhancers	Dnd41	blood
19	chr6:29676200-29676600	Enhancers	GM12878-XiMat	blood
20	chr6:29676200-29676800	Enhancers	Primary B cells from cord blood	blood
21	chr6:29676200-29676800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:29676200-29677600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr6:29676200-29677600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:29676200-29678600	Enhancers	Fetal Thymus	thymus
25	chr6:29676400-29676600	Active TSS	Duodenum Mucosa	Duodenum
26	chr6:29676400-29677000	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr6:29676400-29677200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
28	chr6:29676400-29677400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:29676400-29677600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr6:29676400-29677600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr6:29676400-29677800	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:29676400-29678200	Enhancers	Primary hematopoietic stem cells	blood

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