Variant report

Variant	rs3129056
Chromosome Location	chr6:29670250-29670251
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	chr6:29670114..29670993-chr6:29802276..29803394,5	K562	blood:
2	chr10:38965666..38966167-chr6:29670107..29670640,2	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1610588	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1610742	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1610744	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2107203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535238	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2535274	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2535275	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2747421	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2747427	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2747428	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2747429	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2747430	0.91[AFR][1000 genomes]
rs2747457	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2747460	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2747467	0.94[AFR][1000 genomes]
rs2907897	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3094724	0.93[ASN][1000 genomes]
rs3094725	0.93[ASN][1000 genomes]
rs3094729	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3094730	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3094731	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3094732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3095284	0.93[ASN][1000 genomes]
rs3116799	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3116800	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3116802	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3116803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3116804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3116811	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3116814	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3117295	0.93[ASN][1000 genomes]
rs3117299	0.93[ASN][1000 genomes]
rs3117301	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3117312	0.93[ASN][1000 genomes]
rs3129033	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3129035	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3129036	0.82[ASN][1000 genomes]
rs3129037	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3129039	0.93[ASN][1000 genomes]
rs3129042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3129046	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129048	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129058	0.81[ASN][1000 genomes]
rs3129060	0.80[ASN][1000 genomes]
rs3129061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129062	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129063	0.81[ASN][1000 genomes]
rs3129064	0.80[ASN][1000 genomes]
rs3129065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3129070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129082	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3129084	0.95[ASN][1000 genomes]
rs3129086	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129092	0.95[ASN][1000 genomes]
rs3129189	0.81[ASN][1000 genomes]
rs3131864	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131865	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131867	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3131868	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131873	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131880	0.80[ASN][1000 genomes]
rs3131884	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3131886	0.80[ASN][1000 genomes]
rs3131889	0.85[ASN][1000 genomes]
rs3131890	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131895	0.93[ASN][1000 genomes]
rs3131898	0.91[ASN][1000 genomes]
rs374317	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs375248	0.81[ASN][1000 genomes]
rs375984	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs376319	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs387640	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs387642	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs396660	0.91[AFR][1000 genomes]
rs417764	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs445150	0.91[AFR][1000 genomes]
rs448380	0.81[ASN][1000 genomes]
rs448489	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7776082	0.80[ASN][1000 genomes]
rs9258017	0.93[ASN][1000 genomes]
rs9258048	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258052	0.81[ASN][1000 genomes]
rs9258053	0.80[ASN][1000 genomes]
rs9258062	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9258064	0.81[AMR][1000 genomes]
rs9258068	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258077	0.85[ASN][1000 genomes]
rs9258078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9258079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9258083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258087	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258088	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258103	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9258104	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258107	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9258108	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv519888	chr6:29668537-29673483	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3129056	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3129056	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3129056	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29664000-29690600	Weak transcription	Right Atrium	heart
2	chr6:29670000-29670800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:29670200-29670400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr6:29670200-29670400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:29670200-29670400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr6:29670200-29670400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
7	chr6:29670200-29670600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:29670200-29670600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:29670200-29670600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:29670200-29670800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:29670200-29670800	Enhancers	Liver	Liver
12	chr6:29670200-29671000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr6:29670200-29671000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr6:29670200-29671000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr6:29670200-29678200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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