Variant report

Variant	rs6666953
Chromosome Location	chr1:241912425-241912426
allele	A/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	TFAP2C	chr1:241912323-241913491	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:241912274-241912672	SK-N-MC	brain:	n/a	n/a
3	TFAP2A	chr1:241912340-241913498	Hela-S3	cervix:	n/a	chr1:241912592-241912606 chr1:241912594-241912604 chr1:241912590-241912605 chr1:241912594-241912604 chr1:241912592-241912606
4	RFX5	chr1:241912412-241913887	Hela-S3	cervix:	n/a	chr1:241913724-241913732
5	STAT3	chr1:241912366-241912682	MCF10A-Er-Src	breast:	n/a	n/a
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	SMARCC1	chr1:241912311-241913379	Hela-S3	cervix:	n/a	n/a
13	RAD21	chr1:241912419-241913556	Hela-S3	cervix:	n/a	n/a
14	STAT3	chr1:241912417-241912645	MCF10A-Er-Src	breast:	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	STAT3	chr1:241912355-241912819	Hela-S3	cervix:	n/a	n/a
18	MAX	chr1:241912348-241913600	Hela-S3	cervix:	n/a	chr1:241913078-241913087
19	CEBPB	chr1:241912360-241913937	Hela-S3	cervix:	n/a	chr1:241913764-241913781 chr1:241913464-241913477 chr1:241913465-241913476 chr1:241912428-241912441
20	POLR2A	chr1:241912420-241912659	Hela-S3	cervix:	n/a	n/a
21	TBL1XR1	chr1:241912422-241912499	K562	blood:	n/a	n/a
22	STAT3	chr1:241912316-241912782	MCF10A-Er-Src	breast:	n/a	n/a
23	BRCA1	chr1:241912422-241912977	Hela-S3	cervix:	n/a	chr1:241912553-241912560
24	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: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10737867	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737868	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10737869	0.96[ASN][1000 genomes]
rs10754735	0.83[ASN][1000 genomes]
rs10802988	0.82[ASN][1000 genomes]
rs10802989	0.82[ASN][1000 genomes]
rs10802990	0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10926561	0.84[ASN][1000 genomes]
rs10926563	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10926564	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10926569	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11809239	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12022825	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12038477	0.85[JPT][hapmap]
rs12042255	0.90[JPT][hapmap]
rs12081277	0.84[ASN][1000 genomes]
rs1891566	0.81[ASN][1000 genomes]
rs3922506	0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3922507	0.84[ASN][1000 genomes]
rs4129118	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4428871	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4658661	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs56396922	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6413961	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6429300	0.99[ASN][1000 genomes]
rs6429301	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6429303	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6429304	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429305	0.96[ASN][1000 genomes]
rs6429312	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6429313	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6429314	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6660811	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6669036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669629	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6680142	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6695661	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6695767	0.84[ASN][1000 genomes]
rs6696527	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7368200	0.82[ASN][1000 genomes]
rs7411533	0.92[ASN][1000 genomes]
rs7411702	0.80[YRI][hapmap];0.84[ASN][1000 genomes]
rs7418198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7418599	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs7418764	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7526583	0.90[ASN][1000 genomes]
rs7526586	0.87[ASN][1000 genomes]
rs7530794	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530797	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7533622	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7551270	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9428515	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9428516	0.81[ASN][1000 genomes]
rs9428520	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9428521	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs9428527	0.87[JPT][hapmap]
rs9428898	0.91[JPT][hapmap]
rs9428900	0.91[JPT][hapmap]
rs9428902	0.91[JPT][hapmap]
rs952084	0.86[CHB][hapmap];0.95[JPT][hapmap]

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

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241911000-241912600	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr1:241911400-241912800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:241911600-241912800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:241912000-241912800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:241912000-241912800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:241912000-241913000	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr1:241912000-241913000	Active TSS	Ovary	ovary
8	chr1:241912200-241912600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:241912200-241912600	Active TSS	Brain Anterior Caudate	brain
10	chr1:241912200-241912600	Active TSS	Placenta	Placenta
11	chr1:241912200-241912600	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr1:241912200-241912600	Active TSS	HSMMtube	muscle
13	chr1:241912200-241912600	Active TSS	NHEK	skin
14	chr1:241912200-241912800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:241912200-241912800	Active TSS	Aorta	Aorta
16	chr1:241912200-241912800	Active TSS	Rectal Smooth Muscle	rectum
17	chr1:241912200-241913000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:241912400-241912600	Active TSS	Colon Smooth Muscle	Colon
19	chr1:241912400-241912600	Active TSS	Duodenum Mucosa	Duodenum
20	chr1:241912400-241912600	Flanking Active TSS	HMEC	breast
21	chr1:241912400-241912600	Enhancers	K562	blood
22	chr1:241912400-241912800	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr1:241912400-241912800	Active TSS	Fetal Kidney	kidney
24	chr1:241912400-241913200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:241912400-241913200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr1:241912400-241913200	Active TSS	HSMM	muscle
27	chr1:241912400-241913200	Flanking Active TSS	Osteobl	bone
28	chr1:241912400-241913400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:241912400-241913400	Enhancers	Fetal Heart	heart
30	chr1:241912400-241913400	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:241912400-241913400	Enhancers	A549	lung
32	chr1:241912400-241913600	Flanking Active TSS	Hela-S3	cervix
33	chr1:241912400-241913800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:241912400-241913800	Enhancers	Placenta Amnion	Placenta Amnion

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