Variant report

Variant	rs3131889
Chromosome Location	chr6:29663309-29663310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29615212..29617400-chr6:29662195..29664604,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1610588	0.83[ASN][1000 genomes]
rs1610742	0.83[ASN][1000 genomes]
rs1610744	0.83[ASN][1000 genomes]
rs2107203	0.85[ASN][1000 genomes]
rs2158290	0.85[ASN][1000 genomes]
rs2535238	0.80[ASN][1000 genomes]
rs2535274	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2535275	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2747421	0.80[ASN][1000 genomes]
rs2747427	0.80[ASN][1000 genomes]
rs2747428	0.80[ASN][1000 genomes]
rs2747429	0.80[ASN][1000 genomes]
rs2747457	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2747460	0.87[ASN][1000 genomes]
rs2907897	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3094724	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3094725	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3094729	0.82[ASN][1000 genomes]
rs3094730	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3094731	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3094732	0.85[ASN][1000 genomes]
rs3094734	0.84[ASN][1000 genomes]
rs3095284	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3095290	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3116799	0.81[ASN][1000 genomes]
rs3116802	0.85[ASN][1000 genomes]
rs3116803	0.85[ASN][1000 genomes]
rs3116804	0.84[ASN][1000 genomes]
rs3116811	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3116814	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3117295	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3117299	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3117301	0.87[ASN][1000 genomes]
rs3117312	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3129033	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129035	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129036	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129039	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3129042	0.83[ASN][1000 genomes]
rs3129046	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129047	0.85[ASN][1000 genomes]
rs3129048	0.85[ASN][1000 genomes]
rs3129055	0.85[ASN][1000 genomes]
rs3129056	0.85[ASN][1000 genomes]
rs3129058	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129061	0.85[ASN][1000 genomes]
rs3129062	0.80[ASN][1000 genomes]
rs3129063	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129065	0.85[ASN][1000 genomes]
rs3129066	0.85[ASN][1000 genomes]
rs3129067	0.84[ASN][1000 genomes]
rs3129070	0.85[ASN][1000 genomes]
rs3129072	0.85[ASN][1000 genomes]
rs3129084	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3129086	0.85[ASN][1000 genomes]
rs3129092	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3129189	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130251	0.84[EUR][1000 genomes]
rs3131864	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3131865	0.85[ASN][1000 genomes]
rs3131866	0.85[ASN][1000 genomes]
rs3131867	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3131868	0.85[ASN][1000 genomes]
rs3131870	0.85[ASN][1000 genomes]
rs3131871	0.85[ASN][1000 genomes]
rs3131872	0.85[ASN][1000 genomes]
rs3131873	0.85[ASN][1000 genomes]
rs3131874	0.85[ASN][1000 genomes]
rs3131884	0.86[ASN][1000 genomes]
rs3131890	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131895	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131898	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs374317	0.80[ASN][1000 genomes]
rs375984	0.80[ASN][1000 genomes]
rs376319	0.80[ASN][1000 genomes]
rs387640	0.80[ASN][1000 genomes]
rs387642	0.80[ASN][1000 genomes]
rs417764	0.80[ASN][1000 genomes]
rs448489	0.80[ASN][1000 genomes]
rs9258017	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9258048	0.85[ASN][1000 genomes]
rs9258068	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9258074	0.85[ASN][1000 genomes]
rs9258077	0.84[ASN][1000 genomes]
rs9258078	0.84[ASN][1000 genomes]
rs9258079	0.85[ASN][1000 genomes]
rs9258083	0.85[ASN][1000 genomes]
rs9258087	0.83[ASN][1000 genomes]
rs9258088	0.83[ASN][1000 genomes]
rs9258104	0.85[ASN][1000 genomes]
rs9258107	0.81[ASN][1000 genomes]
rs9258108	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	esv1840790	chr6:29658864-29669830	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
7	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
8	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
9	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
10	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3131889	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3131889	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3131889	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3131889	C6orf12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29662600-29663600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:29662600-29664200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:29662800-29664200	Enhancers	H1 Cell Line	embryonic stem cell

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