Variant report

Variant	rs269403
Chromosome Location	chr1:67342514-67342515
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	RAD21	chr1:67342452-67342631	K562	blood:	n/a	n/a
2	CTCF	chr1:67342495-67342570	MCF-7	breast:	n/a	chr1:67342525-67342538
3	RAD21	chr1:67342416-67342597	HepG2	liver:	n/a	n/a
4	CTCF	chr1:67342438-67342635	H1-hESC	embryonic stem cell:	n/a	chr1:67342525-67342538
5	CTCF	chr1:67342420-67342570	WERI-Rb-1	eye:	n/a	chr1:67342525-67342538
6	RAD21	chr1:67342365-67342647	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr1:67342480-67342630	MCF-7	breast:	n/a	chr1:67342525-67342538
8	CTCF	chr1:67342480-67342630	BJ	skin:	n/a	chr1:67342525-67342538
9	CTCF	chr1:67342467-67342583	NHEK	skin:	n/a	chr1:67342525-67342538
10	CTCF	chr1:67342500-67342650	HMEC	breast:	n/a	chr1:67342525-67342538
11	RAD21	chr1:67342282-67342702	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr1:67342480-67342630	HMF	breast:	n/a	chr1:67342525-67342538
13	CTCF	chr1:67342453-67342596	Hela-S3	cervix:	n/a	chr1:67342525-67342538
14	CTCF	chr1:67342372-67342710	K562	blood:	n/a	chr1:67342525-67342538
15	RAD21	chr1:67342482-67342662	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr1:67342480-67342630	RPTEC	kidney:	n/a	chr1:67342525-67342538
17	CTCF	chr1:67342420-67342570	HMEC	breast:	n/a	chr1:67342525-67342538
18	CTCF	chr1:67342440-67342637	K562	blood:	n/a	chr1:67342525-67342538
19	RAD21	chr1:67342424-67342693	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr1:67342458-67342580	MCF-7	breast:	n/a	chr1:67342525-67342538
21	RAD21	chr1:67342388-67342677	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr1:67342318-67342804	HCT-116	colon:	n/a	n/a
23	CTCF	chr1:67342509-67342587	ProgFib	skin:	n/a	chr1:67342525-67342538
24	RAD21	chr1:67342487-67342566	HepG2	liver:	n/a	n/a
25	CTCF	chr1:67342499-67342566	GM12878	blood:	n/a	chr1:67342525-67342538
26	CTCF	chr1:67342460-67342610	K562	blood:	n/a	chr1:67342525-67342538
27	SMC3	chr1:67342421-67342654	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr1:67342420-67342570	HCPEpiC	choroid plexus:	n/a	chr1:67342525-67342538
29	RAD21	chr1:67342416-67342604	K562	blood:	n/a	n/a
30	CTCF	chr1:67342480-67342630	GM12878	blood:	n/a	chr1:67342525-67342538
31	CTCF	chr1:67342452-67342620	Pancreas_OC	pancreas:	n/a	chr1:67342525-67342538

Variant related genes	Relation type
WDR78	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12239035	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239074	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1280338	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1925399	0.94[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1925400	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1925401	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1925402	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1925403	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[MKK][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1925404	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1925405	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1925406	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1931297	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2147835	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2147836	0.83[CEU][hapmap]
rs269395	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs269399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs269401	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs269402	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs269405	0.82[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2991353	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2991354	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2991359	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4255358	0.82[EUR][1000 genomes]
rs496070	0.89[CEU][hapmap]
rs55858354	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56400880	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs573490	0.88[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs576078	0.81[MKK][hapmap]
rs61467716	0.87[EUR][1000 genomes]
rs6699606	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671671	0.82[EUR][1000 genomes]
rs72671673	0.83[EUR][1000 genomes]
rs72671674	0.80[EUR][1000 genomes]
rs72671675	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671677	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671679	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671680	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671682	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72671685	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7552770	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv830093	chr1:67173594-67348264	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv546443	chr1:67268642-67352960	Genic enhancers Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871738	chr1:67268642-67375206	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv871259	chr1:67275027-67375206	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs269403	MIER1	cis	parietal	SCAN
rs269403	GADD45A	cis	cerebellum	SCAN
rs269403	WDR78	cis	parietal	SCAN
rs269403	WLS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67336200-67344000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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