Variant report

Variant	rs2394173
Chromosome Location	chr6:29773158-29773159
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	RAD21	chr6:29772830-29773206	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr6:29773093-29773238	HepG2	liver:	n/a	chr6:29773145-29773156
3	USF1	chr6:29773007-29773299	H1-hESC	embryonic stem cell:	n/a	chr6:29773145-29773156
4	USF2	chr6:29773033-29773255	Hela-S3	cervix:	n/a	chr6:29773145-29773156
5	USF1	chr6:29772948-29773213	H1-hESC	embryonic stem cell:	n/a	chr6:29773145-29773156
6	CTCF	chr6:29772908-29773160	K562	blood:	n/a	n/a
7	RAD21	chr6:29772839-29773183	H1-hESC	embryonic stem cell:	n/a	n/a
8	USF2	chr6:29773061-29773171	HepG2	liver:	n/a	chr6:29773145-29773156
9	RAD21	chr6:29772890-29773161	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr6:29773020-29773170	GM12869	blood:	n/a	n/a
11	CTCF	chr6:29773040-29773190	GM12871	blood:	n/a	n/a

Variant related genes	Relation type
RPL7AP7	TF binding region

Extended variants
information (count: 113 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1063320	0.85[ASN][1000 genomes]
rs1610677	0.81[ASN][1000 genomes]
rs1610678	0.85[ASN][1000 genomes]
rs1611141	0.83[ASN][1000 genomes]
rs1611149	0.85[ASN][1000 genomes]
rs1611156	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1611157	0.81[ASN][1000 genomes]
rs1611160	0.81[ASN][1000 genomes]
rs1611165	0.81[ASN][1000 genomes]
rs1611173	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611190	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1611475	0.82[ASN][1000 genomes]
rs1620202	0.85[ASN][1000 genomes]
rs1625361	0.85[ASN][1000 genomes]
rs1632943	0.85[ASN][1000 genomes]
rs1632944	0.81[ASN][1000 genomes]
rs1632946	0.81[ASN][1000 genomes]
rs1632947	0.81[ASN][1000 genomes]
rs1632948	0.85[ASN][1000 genomes]
rs1632951	0.81[ASN][1000 genomes]
rs1633040	0.85[ASN][1000 genomes]
rs1633053	0.85[ASN][1000 genomes]
rs1633077	0.85[ASN][1000 genomes]
rs16867712	0.80[AFR][1000 genomes]
rs1710	0.84[ASN][1000 genomes]
rs1736932	0.85[ASN][1000 genomes]
rs1736933	0.81[ASN][1000 genomes]
rs1736935	0.85[ASN][1000 genomes]
rs1736936	0.80[ASN][1000 genomes]
rs1736938	0.80[ASN][1000 genomes]
rs1736940	0.85[ASN][1000 genomes]
rs1736943	0.81[ASN][1000 genomes]
rs1736944	0.85[ASN][1000 genomes]
rs1736947	0.85[ASN][1000 genomes]
rs2249571	0.80[ASN][1000 genomes]
rs2249863	0.81[ASN][1000 genomes]
rs2394688	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517928	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2517929	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2517930	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2517931	0.83[ASN][1000 genomes]
rs2517937	0.85[ASN][1000 genomes]
rs2523409	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523763	0.91[ASN][1000 genomes]
rs2523818	0.80[ASN][1000 genomes]
rs2734982	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2734987	0.90[ASN][1000 genomes]
rs2735022	0.81[ASN][1000 genomes]
rs2735027	0.85[ASN][1000 genomes]
rs2735030	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735035	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2735038	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2735043	0.85[ASN][1000 genomes]
rs2735048	0.83[ASN][1000 genomes]
rs2735049	0.83[ASN][1000 genomes]
rs2743930	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2743936	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2743940	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2743943	0.80[ASN][1000 genomes]
rs2743945	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844821	0.81[ASN][1000 genomes]
rs2844835	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844841	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844843	0.85[ASN][1000 genomes]
rs2844844	0.83[ASN][1000 genomes]
rs2905756	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2975033	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2975034	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2975035	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2975038	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3094560	0.83[ASN][1000 genomes]
rs3094643	0.89[ASN][1000 genomes]
rs3115627	0.89[ASN][1000 genomes]
rs3128914	0.81[ASN][1000 genomes]
rs34260811	0.80[AFR][1000 genomes]
rs35674592	0.81[ASN][1000 genomes]
rs4711200	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713250	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4993665	0.82[ASN][1000 genomes]
rs4993667	0.83[ASN][1000 genomes]
rs6457057	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6457058	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6911139	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6934957	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7776026	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9295821	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9357085	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9366749	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9380139	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380141	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380142	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380143	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380145	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	esv11180	chr6:29729381-29800066	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	esv3423001	chr6:29733216-29878601	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	esv3475027	chr6:29733297-29922699	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	esv3475028	chr6:29733297-29922699	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	esv3420260	chr6:29734457-29835593	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	esv3330285	chr6:29736281-29881328	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv883539	chr6:29748206-29780529	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	esv3396224	chr6:29754243-29888093	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
16	nsv965702	chr6:29758408-29798943	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
18	esv3426050	chr6:29761594-29918407	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
19	esv3431350	chr6:29765473-29922767	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
20	nsv883540	chr6:29772395-29784317	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2394173	MLN	cis	parietal	SCAN
rs2394173	ZSCAN23	cis	parietal	SCAN
rs2394173	HIST1H2AI	cis	parietal	SCAN
rs2394173	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs2394173	HCG4P6	Cis_1M	lymphoblastoid	RTeQTL
rs2394173	BTN2A1	cis	cerebellum	SCAN
rs2394173	HLA-H	cis	lymphoblastoid	seeQTL
rs2394173	HLA.A29.1	cis	multi-tissue	Pritchard
rs2394173	HIST1H2AH	cis	cerebellum	SCAN
rs2394173	HIST1H4F	cis	parietal	SCAN
rs2394173	HLA-A	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29764800-29780600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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