Variant report

Variant	rs4072425
Chromosome Location	chr1:153588843-153588844
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	MAX	chr1:153588652-153589753	ECC-1	luminal epithelium:	n/a	chr1:153589522-153589535 chr1:153588848-153588858 chr1:153589523-153589534 chr1:153589525-153589534 chr1:153589524-153589534 chr1:153589526-153589533 chr1:153589519-153589538 chr1:153589719-153589728 chr1:153589524-153589533 chr1:153589522-153589535 chr1:153589523-153589534 chr1:153589523-153589534
2	MAZ	chr1:153588783-153589336	K562	blood:	n/a	chr1:153588848-153588858
3	FOS	chr1:153588802-153589028	MCF10A-Er-Src	breast:	n/a	n/a
4	RCOR1	chr1:153588625-153590540	Hela-S3	cervix:	n/a	n/a
5	MYC	chr1:153588632-153589880	MCF10A-Er-Src	breast:	n/a	chr1:153589522-153589535 chr1:153588848-153588858 chr1:153589523-153589534 chr1:153589525-153589534 chr1:153589524-153589534 chr1:153589526-153589533 chr1:153589519-153589538 chr1:153589719-153589728 chr1:153589524-153589533 chr1:153589522-153589535 chr1:153589523-153589534 chr1:153589523-153589534
6	POLR2A	chr1:153588755-153590626	Hela-S3	cervix:	n/a	n/a
7	FOS	chr1:153588711-153589099	MCF10A-Er-Src	breast:	n/a	chr1:153589025-153589037
8	CEBPB	chr1:153588750-153589033	K562	blood:	n/a	n/a
9	TCF7L2	chr1:153588665-153589364	Hela-S3	cervix:	n/a	n/a
10	NR2F2	chr1:153588516-153589794	MCF-7	breast:	n/a	n/a
11	POLR2A	chr1:153588524-153589044	MCF-7	breast:	n/a	n/a
12	SMC3	chr1:153588656-153589251	Hela-S3	cervix:	n/a	n/a
13	CHD2	chr1:153588696-153590501	Hela-S3	cervix:	n/a	n/a
14	MYC	chr1:153588787-153589104	K562	blood:	n/a	chr1:153588848-153588858
15	POLR2A	chr1:153588533-153589153	ECC-1	luminal epithelium:	n/a	n/a
16	ZNF143	chr1:153588804-153589347	Hela-S3	cervix:	n/a	n/a
17	TBP	chr1:153588705-153588880	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:153588800-153588895	HepG2	liver:	n/a	n/a
19	CTCF	chr1:153588760-153588910	NHEK	skin:	n/a	n/a
20	POLR2A	chr1:153588624-153589005	ECC-1	luminal epithelium:	n/a	n/a
21	YY1	chr1:153588669-153588992	HCT-116	colon:	n/a	n/a
22	MAX	chr1:153588734-153589195	K562	blood:	n/a	chr1:153588848-153588858
23	FOS	chr1:153588725-153589099	MCF10A-Er-Src	breast:	n/a	chr1:153589025-153589037
24	POLR2A	chr1:153587509-153589202	MCF-7	breast:	n/a	n/a
25	NFIC	chr1:153588553-153589249	ECC-1	luminal epithelium:	n/a	n/a
26	RFX5	chr1:153588696-153589201	Hela-S3	cervix:	n/a	n/a
27	GTF2F1	chr1:153588633-153589190	Hela-S3	cervix:	n/a	n/a
28	ZBTB7A	chr1:153588757-153589014	K562	blood:	n/a	n/a
29	POLR2A	chr1:153588749-153590574	Hela-S3	cervix:	n/a	n/a
30	MYC	chr1:153588836-153589020	MCF-7	breast:	n/a	chr1:153588848-153588858
31	CEBPB	chr1:153588679-153589046	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr1:153588566-153589182	MCF10A-Er-Src	breast:	n/a	n/a
33	MAX	chr1:153588702-153589377	HepG2	liver:	n/a	chr1:153588848-153588858
34	MAX	chr1:153588502-153589850	MCF-7	breast:	n/a	chr1:153589522-153589535 chr1:153588848-153588858 chr1:153589523-153589534 chr1:153589525-153589534 chr1:153589524-153589534 chr1:153589526-153589533 chr1:153589519-153589538 chr1:153589719-153589728 chr1:153589524-153589533 chr1:153589522-153589535 chr1:153589523-153589534 chr1:153589523-153589534
35	MAX	chr1:153588635-153589288	HepG2	liver:	n/a	chr1:153588848-153588858
36	STAT3	chr1:153588791-153589082	MCF10A-Er-Src	breast:	n/a	chr1:153588836-153588848 chr1:153588835-153588847
37	NR2F2	chr1:153588613-153589162	MCF-7	breast:	n/a	n/a
38	MAX	chr1:153588614-153589817	ECC-1	luminal epithelium:	n/a	chr1:153589522-153589535 chr1:153588848-153588858 chr1:153589523-153589534 chr1:153589525-153589534 chr1:153589524-153589534 chr1:153589526-153589533 chr1:153589519-153589538 chr1:153589719-153589728 chr1:153589524-153589533 chr1:153589522-153589535 chr1:153589523-153589534 chr1:153589523-153589534
39	POLR2A	chr1:153588562-153589127	MCF-7	breast:	n/a	n/a
40	POLR2A	chr1:153588631-153590564	Hela-S3	cervix:	n/a	n/a
41	CEBPB	chr1:153588734-153589043	HepG2	liver:	n/a	n/a
42	RCOR1	chr1:153588797-153588997	K562	blood:	n/a	n/a
43	POLR2A	chr1:153588411-153589077	HCT-116	colon:	n/a	n/a
44	MAX	chr1:153588843-153589077	HepG2	liver:	n/a	chr1:153588848-153588858
45	CEBPB	chr1:153588678-153589097	Hela-S3	cervix:	n/a	n/a
46	NFIC	chr1:153588498-153589837	ECC-1	luminal epithelium:	n/a	n/a
47	CEBPB	chr1:153588565-153589162	ECC-1	luminal epithelium:	n/a	n/a
48	CEBPB	chr1:153588478-153589261	HCT-116	colon:	n/a	n/a
49	SMARCB1	chr1:153588584-153590492	Hela-S3	cervix:	n/a	n/a
50	MAZ	chr1:153588566-153590472	Hela-S3	cervix:	n/a	chr1:153589522-153589535 chr1:153588848-153588858 chr1:153589523-153589534 chr1:153589525-153589534 chr1:153589524-153589534 chr1:153589526-153589533 chr1:153589519-153589538 chr1:153589719-153589728 chr1:153589524-153589533 chr1:153589522-153589535 chr1:153589523-153589534 chr1:153589523-153589534

No.	Distal block	Cell Line	Cell type
1	chr1:153588609..153589299-chr12:113771908..113772428,2	Hela-S3	cervix:
2	chr1:153587320..153590389-chr1:153961977..153964673,3	MCF-7	breast:
3	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
4	chr1:153586138..153590435-chr1:153962533..153966036,4	K562	blood:
5	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
6	chr1:153587775..153589885-chr1:153631112..153632805,2	MCF-7	breast:
7	chr1:153518882..153521795-chr1:153587475..153590405,3	MCF-7	breast:
8	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:

Variant related genes	Relation type
S100A14	TF binding region
S100A16	TF binding region
ENSG00000196754	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000188015	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000089060	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs1046381	0.84[ASN][1000 genomes]
rs10797096	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs10908848	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs11265625	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11497739	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11548102	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11548103	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548104	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11588347	0.83[EUR][1000 genomes]
rs12139953	0.83[EUR][1000 genomes]
rs12730186	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28416529	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28518786	0.89[EUR][1000 genomes]
rs28754733	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35760493	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35890901	0.81[ASN][1000 genomes]
rs3806233	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3862047	0.85[CEU][hapmap];0.80[CHD][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4515830	0.88[CEU][hapmap]
rs4845563	0.85[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs4845564	0.83[EUR][1000 genomes]
rs55772653	0.85[EUR][1000 genomes]
rs66721814	0.86[EUR][1000 genomes]
rs6674929	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs9330298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9330299	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330300	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9330301	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9660679	0.96[ASN][1000 genomes]
rs9662664	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs9699949	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9700179	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9700928	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9726753	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9729773	0.96[ASN][1000 genomes]
rs9792913	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9792963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9792967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793310	0.96[ASN][1000 genomes]
rs999418	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4072425	SCNM1	cis	parietal	SCAN
rs4072425	S100A2	cis	cerebellum	SCAN
rs4072425	S100A13	cis	parietal	SCAN
rs4072425	RP1-178F15.4	cis	Thyroid	GTEx
rs4072425	S100A16	cis	Muscle Skeletal	GTEx
rs4072425	CTSS	cis	parietal	SCAN
rs4072425	CHTOP	cis	Muscle Skeletal	GTEx
rs4072425	S100A16	cis	parietal	SCAN
rs4072425	S100A16	cis	cerebellum	SCAN
rs4072425	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs4072425	S100A14	cis	Esophagus Mucosa	GTEx
rs4072425	S100A10	cis	cerebellum	SCAN
rs4072425	SLC27A3	cis	cerebellum	SCAN
rs4072425	S100A13	cis	lymphoblastoid	seeQTL
rs4072425	FLG	cis	cerebellum	SCAN
rs4072425	S100A9	cis	parietal	SCAN
rs4072425	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs4072425	RP1-178F15.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153582800-153591200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:153583000-153589000	Active TSS	Esophagus	oesophagus
3	chr1:153583600-153590000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:153585000-153589200	Weak transcription	Brain Angular Gyrus	brain
5	chr1:153585400-153589000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:153585400-153589800	Weak transcription	Brain Substantia Nigra	brain
7	chr1:153585600-153589400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:153585600-153590400	Enhancers	Lung	lung
9	chr1:153585600-153590600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:153585600-153591000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:153585600-153591200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:153585600-153591400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:153585600-153592200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:153585600-153596400	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:153585600-153597600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:153585600-153598800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:153585600-153599000	Weak transcription	Aorta	Aorta
18	chr1:153585800-153599200	Weak transcription	Fetal Brain Male	brain
19	chr1:153586000-153589000	Weak transcription	Ovary	ovary
20	chr1:153586000-153589400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:153586000-153589600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:153586000-153589800	Weak transcription	Brain Anterior Caudate	brain
23	chr1:153586000-153590000	Weak transcription	HUVEC	blood vessel
24	chr1:153586000-153591000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:153586000-153591000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:153586000-153591000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:153586000-153595600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:153586000-153596200	Weak transcription	Fetal Kidney	kidney
29	chr1:153586000-153598800	Weak transcription	Psoas Muscle	Psoas
30	chr1:153586200-153589000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:153586200-153589000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:153586200-153589000	Weak transcription	HSMM	muscle
33	chr1:153586200-153589000	Weak transcription	HSMMtube	muscle
34	chr1:153586200-153591000	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:153586200-153591400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:153586200-153591600	Weak transcription	NH-A	brain
37	chr1:153586800-153590400	Enhancers	Spleen	Spleen
38	chr1:153587000-153589000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:153587000-153589000	Weak transcription	NHDF-Ad	bronchial
40	chr1:153587000-153589800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:153587200-153590400	Weak transcription	Osteobl	bone
42	chr1:153587400-153589000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:153587400-153589400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:153587600-153589200	Active TSS	Rectal Smooth Muscle	rectum
45	chr1:153587600-153590400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:153587600-153590400	Enhancers	Pancreas	Pancrea
47	chr1:153587800-153589000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr1:153588000-153589000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:153588000-153589800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:153588000-153590000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin

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