Variant report

Variant	rs11497739
Chromosome Location	chr1:153583066-153583067
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	SMC3	chr1:153582814-153583214	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:153578781-153585928	U87	brain:	n/a	n/a
3	STAT3	chr1:153582910-153583110	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:153580416-153585950	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr1:153582815-153583176	Hela-S3	cervix:	n/a	n/a
6	CHD2	chr1:153582766-153583724	Hela-S3	cervix:	n/a	chr1:153583305-153583315
7	MAX	chr1:153582744-153583772	MCF-7	breast:	n/a	chr1:153583503-153583514 chr1:153583503-153583514 chr1:153583499-153583518 chr1:153583504-153583513 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583512 chr1:153583503-153583514 chr1:153583502-153583515 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583514
8	POLR2A	chr1:153581091-153584061	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:153582864-153583151	Hela-S3	cervix:	n/a	n/a
10	E2F4	chr1:153582719-153583157	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr1:153582752-153583159	MCF10A-Er-Src	breast:	n/a	chr1:153583120-153583129 chr1:153582957-153582965 chr1:153582957-153582964
12	POLR2A	chr1:153581118-153584087	Hela-S3	cervix:	n/a	n/a
13	RAD21	chr1:153582849-153583161	Hela-S3	cervix:	n/a	chr1:153583028-153583038 chr1:153583026-153583038 chr1:153582976-153582990
14	TCF12	chr1:153582459-153583685	MCF-7	breast:	n/a	chr1:153583298-153583308 chr1:153583031-153583041
15	MAX	chr1:153582672-153584061	Hela-S3	cervix:	n/a	chr1:153583503-153583514 chr1:153583503-153583514 chr1:153583499-153583518 chr1:153583504-153583513 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583512 chr1:153583503-153583514 chr1:153583502-153583515 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583514
16	SMARCC2	chr1:153581117-153583552	Hela-S3	cervix:	n/a	n/a
17	STAT3	chr1:153582524-153583659	MCF10A-Er-Src	breast:	n/a	chr1:153583609-153583621 chr1:153582822-153582834
18	POLR2A	chr1:153578145-153583129	HUVEC	blood vessel:	n/a	n/a
19	JUND	chr1:153582770-153583111	A549	lung:	n/a	chr1:153582957-153582965 chr1:153582957-153582964
20	JUND	chr1:153582817-153583119	K562	blood:	n/a	chr1:153582957-153582965 chr1:153582957-153582964
21	POLR2A	chr1:153582647-153583307	U87	brain:	n/a	n/a
22	TBP	chr1:153582903-153583130	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:153582935-153583244	MCF-7	breast:	n/a	n/a
24	TFAP2A	chr1:153582659-153583571	Hela-S3	cervix:	n/a	chr1:153583077-153583088 chr1:153583075-153583089 chr1:153583077-153583088 chr1:153583077-153583088 chr1:153583073-153583088 chr1:153583077-153583088
25	POLR2A	chr1:153582647-153583273	U87	brain:	n/a	n/a
26	FOS	chr1:153582762-153583157	MCF10A-Er-Src	breast:	n/a	chr1:153583120-153583129 chr1:153582957-153582965 chr1:153582957-153582964
27	SRF	chr1:153582911-153583068	K562	blood:	n/a	n/a
28	POLR2A	chr1:153582332-153584090	HCT-116	colon:	n/a	n/a
29	GATA3	chr1:153582870-153583372	T-47D	breast:	n/a	n/a
30	TCF12	chr1:153582709-153583268	SK-N-SH	brain:	n/a	chr1:153583031-153583041
31	MXI1	chr1:153582860-153583156	Hela-S3	cervix:	n/a	n/a
32	MAX	chr1:153582767-153583143	K562	blood:	n/a	n/a
33	GATA3	chr1:153582681-153583697	MCF-7	breast:	n/a	chr1:153582836-153582846
34	GTF2F1	chr1:153582364-153583618	Hela-S3	cervix:	n/a	n/a
35	NR2F2	chr1:153582663-153583454	MCF-7	breast:	n/a	n/a
36	TAF1	chr1:153582732-153583187	Hela-S3	cervix:	n/a	n/a
37	GATA3	chr1:153582940-153583305	T-47D	breast:	n/a	n/a
38	POLR2A	chr1:153582841-153583953	MCF10A-Er-Src	breast:	n/a	n/a
39	ZNF217	chr1:153582998-153583223	MCF-7	breast:	n/a	n/a
40	FOS	chr1:153582795-153583153	MCF10A-Er-Src	breast:	n/a	chr1:153583120-153583129 chr1:153582957-153582965 chr1:153582957-153582964
41	SMARCB1	chr1:153582344-153583905	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:153580356-153583237	HepG2	liver:	n/a	n/a
43	NR2F2	chr1:153582711-153583692	MCF-7	breast:	n/a	n/a
44	GATA2	chr1:153581193-153583269	HUVEC	blood vessel:	n/a	chr1:153581551-153581560 chr1:153582836-153582846
45	JUN	chr1:153582952-153583175	K562	blood:	n/a	chr1:153583120-153583129 chr1:153582957-153582965 chr1:153582957-153582964
46	GATA3	chr1:153582858-153583467	MCF-7	breast:	n/a	n/a
47	MAZ	chr1:153583058-153583271	K562	blood:	n/a	n/a
48	TFAP2C	chr1:153582744-153583697	Hela-S3	cervix:	n/a	chr1:153583073-153583088
49	MYC	chr1:153582822-153584034	MCF10A-Er-Src	breast:	n/a	chr1:153583503-153583514 chr1:153583503-153583514 chr1:153583499-153583518 chr1:153583504-153583513 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583512 chr1:153583503-153583514 chr1:153583502-153583515 chr1:153583504-153583514 chr1:153583502-153583515 chr1:153583503-153583514
50	POLR2A	chr1:153582804-153583893	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153581285..153583404-chr1:153640253..153643290,3	MCF-7	breast:
2	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
3	chr1:153505889..153508485-chr1:153582874..153585873,3	MCF-7	breast:
4	chr1:153361209..153363367-chr1:153582574..153585428,2	MCF-7	breast:
5	chr1:153582758..153584340-chr1:153640785..153643279,2	K562	blood:
6	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
7	chr1:153518244..153520896-chr1:153581745..153584776,3	MCF-7	breast:
8	chr1:153329994..153332051-chr1:153582439..153585039,2	MCF-7	breast:
9	chr1:153581488..153584174-chr1:153940194..153943077,2	MCF-7	breast:
10	chr1:153580088..153583370-chr1:153747776..153750328,4	MCF-7	breast:
11	chr1:153579256..153583611-chr1:153630358..153635573,4	MCF-7	breast:
12	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
13	chr1:153515934..153518266-chr1:153581311..153583180,3	MCF-7	breast:
14	chr1:153539321..153541162-chr1:153580987..153583409,2	K562	blood:
15	chr1:153524896..153526956-chr1:153582984..153585542,2	MCF-7	breast:
16	chr1:153325873..153327403-chr1:153582234..153585086,2	MCF-7	breast:
17	chr1:153582681..153583443-chr12:46120700..46121359,2	Hela-S3	cervix:
18	chr1:153488074..153490383-chr1:153582465..153584577,2	MCF-7	breast:

Variant related genes	Relation type
S100A16	TF binding region
ENSG00000196754	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1046381	0.82[ASN][1000 genomes]
rs10797056	0.82[TSI][hapmap]
rs11548102	0.96[ASN][1000 genomes]
rs11548103	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12564925	0.82[TSI][hapmap]
rs1411273	0.87[EUR][1000 genomes]
rs1888115	0.82[TSI][hapmap]
rs2274739	0.82[TSI][hapmap]
rs2274740	0.82[TSI][hapmap]
rs28380060	0.82[TSI][hapmap]
rs28416529	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28580554	0.82[TSI][hapmap]
rs28754733	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35760493	0.94[ASN][1000 genomes]
rs3790411	0.96[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs3790412	0.82[TSI][hapmap]
rs3795396	0.82[TSI][hapmap]
rs3806233	0.95[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3818632	0.82[TSI][hapmap]
rs3828031	0.82[TSI][hapmap]
rs4072425	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7345	0.82[TSI][hapmap]
rs7934	0.82[TSI][hapmap]
rs913860	0.82[TSI][hapmap]
rs913861	0.82[TSI][hapmap]
rs9330298	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9330299	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330300	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9330301	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9660679	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9699949	0.95[ASN][1000 genomes]
rs9700179	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9700928	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9726753	0.96[ASN][1000 genomes]
rs9729773	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9792913	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9792963	0.96[ASN][1000 genomes]
rs9792967	0.96[ASN][1000 genomes]
rs9793310	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs985242	0.87[EUR][1000 genomes]
rs999418	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11497739	S100A13	cis	lymphoblastoid	seeQTL
rs11497739	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs11497739	S100A13	cis	parietal	SCAN
rs11497739	CHTOP	cis	Muscle Skeletal	GTEx
rs11497739	S100A14	cis	Thyroid	GTEx
rs11497739	S100A16	cis	cerebellum	SCAN
rs11497739	S100A10	cis	cerebellum	SCAN
rs11497739	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs11497739	S100A16	cis	parietal	SCAN
rs11497739	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs11497739	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs11497739	CTSS	cis	parietal	SCAN
rs11497739	SLC27A3	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153578800-153584800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:153579400-153583600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:153579800-153583600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:153580200-153584800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:153580400-153583200	Transcr. at gene 5' and 3'	NHEK	skin
6	chr1:153580600-153583200	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr1:153580600-153583600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:153580800-153583200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:153580800-153583200	Flanking Active TSS	Colonic Mucosa	Colon
10	chr1:153580800-153583600	Flanking Active TSS	Osteobl	bone
11	chr1:153581000-153583200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:153581000-153583400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr1:153581000-153584000	Enhancers	Colon Smooth Muscle	Colon
14	chr1:153581000-153584200	Enhancers	Fetal Lung	lung
15	chr1:153581200-153584200	Enhancers	Gastric	stomach
16	chr1:153581200-153584200	Enhancers	Pancreas	Pancrea
17	chr1:153581400-153583600	Enhancers	Ovary	ovary
18	chr1:153581400-153584200	Enhancers	Left Ventricle	heart
19	chr1:153581400-153584800	Enhancers	Fetal Heart	heart
20	chr1:153581600-153583200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:153581600-153583200	Flanking Active TSS	HMEC	breast
22	chr1:153581600-153584000	Enhancers	Spleen	Spleen
23	chr1:153581800-153583200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr1:153581800-153583600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:153581800-153583600	Enhancers	Placenta	Placenta
26	chr1:153581800-153583600	Flanking Active TSS	A549	lung
27	chr1:153581800-153584200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:153581800-153584200	Enhancers	Fetal Muscle Trunk	muscle
29	chr1:153581800-153584200	Enhancers	Fetal Muscle Leg	muscle
30	chr1:153581800-153584200	Enhancers	Right Atrium	heart
31	chr1:153581800-153584200	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr1:153581800-153584400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:153582000-153583200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:153582000-153583200	Flanking Active TSS	HepG2	liver
35	chr1:153582000-153583200	Flanking Active TSS	HSMMtube	muscle
36	chr1:153582000-153583400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:153582000-153583400	Enhancers	Adipose Nuclei	Adipose
38	chr1:153582000-153583600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:153582000-153583600	Enhancers	Brain Hippocampus Middle	brain
40	chr1:153582000-153583600	Genic enhancers	Fetal Intestine Small	intestine
41	chr1:153582000-153583800	Weak transcription	Fetal Kidney	kidney
42	chr1:153582000-153584000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:153582000-153584000	Enhancers	Brain Anterior Caudate	brain
44	chr1:153582000-153584000	Enhancers	Fetal Intestine Large	intestine
45	chr1:153582000-153584200	Weak transcription	Aorta	Aorta
46	chr1:153582000-153584200	Enhancers	Lung	lung
47	chr1:153582000-153584400	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr1:153582200-153583400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:153582200-153583400	Enhancers	Psoas Muscle	Psoas
50	chr1:153582200-153583800	Enhancers	Skeletal Muscle Female	skeletal muscle

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