Variant report

Variant	rs6669629
Chromosome Location	chr1:241912674-241912675
allele	A/C
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	TFAP2C	chr1:241912323-241913491	Hela-S3	cervix:	n/a	n/a
2	TFAP2A	chr1:241912340-241913498	Hela-S3	cervix:	n/a	chr1:241912592-241912606 chr1:241912594-241912604 chr1:241912590-241912605 chr1:241912594-241912604 chr1:241912592-241912606
3	RFX5	chr1:241912412-241913887	Hela-S3	cervix:	n/a	chr1:241913724-241913732
4	STAT3	chr1:241912366-241912682	MCF10A-Er-Src	breast:	n/a	n/a
5	FOXA1	chr1:241912446-241912767	T-47D	breast:	n/a	chr1:241912630-241912642
6	MAX	chr1:241912418-241913787	Hela-S3	cervix:	n/a	chr1:241913078-241913087 chr1:241913766-241913775
7	SMARCC2	chr1:241912309-241913422	Hela-S3	cervix:	n/a	n/a
8	RCOR1	chr1:241912364-241913970	Hela-S3	cervix:	n/a	n/a
9	STAT3	chr1:241912399-241912734	MCF10A-Er-Src	breast:	n/a	n/a
10	ZKSCAN1	chr1:241912367-241912823	Hela-S3	cervix:	n/a	n/a
11	EP300	chr1:241912350-241912994	Hela-S3	cervix:	n/a	n/a
12	MYC	chr1:241912579-241912751	MCF10A-Er-Src	breast:	n/a	n/a
13	SMARCC1	chr1:241912311-241913379	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr1:241912419-241913556	Hela-S3	cervix:	n/a	n/a
15	MAFK	chr1:241912383-241913888	Hela-S3	cervix:	n/a	chr1:241912417-241912433 chr1:241912422-241912433 chr1:241912422-241912433 chr1:241912421-241912432 chr1:241912420-241912434
16	TBP	chr1:241912403-241913881	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr1:241912447-241913519	Hela-S3	cervix:	n/a	n/a
18	FOS	chr1:241912482-241912729	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:241912504-241912686	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr1:241912355-241912819	Hela-S3	cervix:	n/a	n/a
21	MAX	chr1:241912348-241913600	Hela-S3	cervix:	n/a	chr1:241913078-241913087
22	CEBPB	chr1:241912360-241913937	Hela-S3	cervix:	n/a	chr1:241913764-241913781 chr1:241913464-241913477 chr1:241913465-241913476 chr1:241912428-241912441
23	MAZ	chr1:241912449-241913386	Hela-S3	cervix:	n/a	chr1:241913078-241913087
24	USF2	chr1:241912437-241912726	Hela-S3	cervix:	n/a	n/a
25	GTF2F1	chr1:241912446-241913576	Hela-S3	cervix:	n/a	n/a
26	STAT3	chr1:241912316-241912782	MCF10A-Er-Src	breast:	n/a	n/a
27	FOS	chr1:241912478-241912730	MCF10A-Er-Src	breast:	n/a	n/a
28	BRCA1	chr1:241912422-241912977	Hela-S3	cervix:	n/a	chr1:241912553-241912560
29	SMC3	chr1:241912339-241913905	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:241796344..241797874-chr1:241911347..241912847,2	K562	blood:
2	chr1:241801200..241805205-chr1:241910998..241914529,7	MCF-7	breast:
3	chr1:241799844..241805446-chr1:241909864..241915090,9	MCF-7	breast:

Variant related genes	Relation type
WDR64	TF binding region
ENSG00000054277	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10737867	0.99[ASN][1000 genomes]
rs10737868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10737869	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10754735	0.81[ASN][1000 genomes]
rs10802988	0.81[ASN][1000 genomes]
rs10802989	0.81[ASN][1000 genomes]
rs10802990	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs10926561	0.83[ASN][1000 genomes]
rs10926563	0.96[ASN][1000 genomes]
rs10926564	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs10926569	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11809239	0.85[ASN][1000 genomes]
rs12022825	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12038477	0.90[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs12042255	0.89[JPT][hapmap]
rs12081277	0.83[ASN][1000 genomes]
rs1418764	0.84[EUR][1000 genomes]
rs1891566	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3922506	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3922507	0.83[ASN][1000 genomes]
rs4129118	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4428871	0.81[ASN][1000 genomes]
rs4658661	0.86[JPT][hapmap]
rs56396922	0.90[ASN][1000 genomes]
rs6413961	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6429300	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429301	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6429304	0.99[ASN][1000 genomes]
rs6429305	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6429313	0.81[ASN][1000 genomes]
rs6429314	0.80[ASN][1000 genomes]
rs6660811	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs6666953	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6669036	0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6680142	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs6695661	0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs6695767	0.83[ASN][1000 genomes]
rs6696527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7368200	0.84[ASN][1000 genomes]
rs7411533	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7411702	0.83[ASN][1000 genomes]
rs7418198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7418599	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7418764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7526583	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7526586	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7530794	0.99[ASN][1000 genomes]
rs7530797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533622	0.80[ASN][1000 genomes]
rs7551270	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9428515	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9428516	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9428520	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs9428521	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs9428527	0.90[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9428891	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9428894	0.84[CHD][hapmap]
rs9428898	0.95[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs9428900	0.95[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs9428902	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs952084	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[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	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS 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	37 gene(s)	inside rSNPs	diseases
4	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv528015	chr1:241865219-242070731	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv2762521	chr1:241891040-242074222	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6669629	ZP4	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241911400-241912800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:241911600-241912800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:241912000-241912800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:241912000-241912800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:241912000-241913000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr1:241912000-241913000	Active TSS	Ovary	ovary
7	chr1:241912200-241912800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:241912200-241912800	Active TSS	Aorta	Aorta
9	chr1:241912200-241912800	Active TSS	Rectal Smooth Muscle	rectum
10	chr1:241912200-241913000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:241912400-241912800	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr1:241912400-241912800	Active TSS	Fetal Kidney	kidney
13	chr1:241912400-241913200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:241912400-241913200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr1:241912400-241913200	Active TSS	HSMM	muscle
16	chr1:241912400-241913200	Flanking Active TSS	Osteobl	bone
17	chr1:241912400-241913400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:241912400-241913400	Enhancers	Fetal Heart	heart
19	chr1:241912400-241913400	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:241912400-241913400	Enhancers	A549	lung
21	chr1:241912400-241913600	Flanking Active TSS	Hela-S3	cervix
22	chr1:241912400-241913800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:241912400-241913800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr1:241912600-241912800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:241912600-241912800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:241912600-241912800	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr1:241912600-241912800	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr1:241912600-241912800	Active TSS	HMEC	breast
29	chr1:241912600-241913400	Flanking Active TSS	Placenta	Placenta
30	chr1:241912600-241913400	Flanking Active TSS	HSMMtube	muscle
31	chr1:241912600-241913400	Flanking Active TSS	NHEK	skin
32	chr1:241912600-241913600	Weak transcription	Brain Anterior Caudate	brain
33	chr1:241912600-241914000	Enhancers	Brain Angular Gyrus	brain

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