Variant report

Variant	rs9258126
Chromosome Location	chr6:29675791-29675792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000225864	Chromatin interaction
ENSG00000204642	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1122947	0.87[EUR][1000 genomes]
rs1984840	0.87[EUR][1000 genomes]
rs2079898	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517913	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517938	0.80[EUR][1000 genomes]
rs2517941	0.82[EUR][1000 genomes]
rs2517943	0.82[EUR][1000 genomes]
rs2523401	0.82[EUR][1000 genomes]
rs2535245	0.81[EUR][1000 genomes]
rs2535246	0.87[EUR][1000 genomes]
rs2735063	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2743925	0.84[EUR][1000 genomes]
rs2743950	0.82[EUR][1000 genomes]
rs2747425	0.82[EUR][1000 genomes]
rs2747453	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2747455	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2844833	0.85[EUR][1000 genomes]
rs29231	0.82[EUR][1000 genomes]
rs29273	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2982837	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3095287	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3129041	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129074	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3129087	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3129090	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131879	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131881	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131882	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6456993	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6941117	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs730858	0.82[EUR][1000 genomes]
rs7738159	0.89[ASN][1000 genomes]
rs7776296	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9257931	0.82[EUR][1000 genomes]
rs9258093	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9258094	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258102	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258106	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9258110	0.86[ASN][1000 genomes]
rs9258111	0.89[ASN][1000 genomes]
rs9258114	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258131	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9258126	HIST1H2BE	cis	parietal	SCAN
rs9258126	HLA-H	cis	multi-tissue	Pritchard
rs9258126	HLA-A	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 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	chr6:29673200-29675800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr6:29673200-29676200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:29673200-29676400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:29673200-29677000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr6:29673400-29676000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr6:29673400-29676200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:29673400-29676200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr6:29673400-29676400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr6:29673400-29678600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:29673600-29676000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:29673600-29676200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:29673600-29676400	Enhancers	Primary T cells from cord blood	blood
16	chr6:29673600-29676800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:29674000-29676000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr6:29674200-29676000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:29674200-29676600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:29674800-29677200	Weak transcription	Spleen	Spleen
21	chr6:29675400-29677800	Flanking Active TSS	Thymus	Thymus
22	chr6:29675600-29676000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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