Variant report

Variant	rs12539263
Chromosome Location	chr7:112121882-112121883
allele	G/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	USF1	chr7:112121850-112122296	A549	lung:	n/a	n/a
2	MAFK	chr7:112121876-112122396	K562	blood:	n/a	chr7:112121919-112121933
3	USF1	chr7:112121828-112122293	A549	lung:	n/a	n/a
4	CEBPB	chr7:112121852-112122639	Hela-S3	cervix:	n/a	n/a
5	MAX	chr7:112121440-112122400	SK-N-SH	brain:	n/a	chr7:112121586-112121595 chr7:112122126-112122135 chr7:112122125-112122134 chr7:112121585-112121594
6	USF1	chr7:112121790-112122312	SK-N-SH	brain:	n/a	n/a
7	TEAD4	chr7:112121721-112122327	MCF-7	breast:	n/a	n/a
8	JUND	chr7:112121715-112122406	MCF-7	breast:	n/a	chr7:112122127-112122134 chr7:112122126-112122134 chr7:112122370-112122382 chr7:112122126-112122135 chr7:112122338-112122348
9	GATA3	chr7:112121791-112122246	SH-SY5Y	brain:	n/a	n/a
10	FOSL1	chr7:112121768-112122528	HCT-116	colon:	n/a	chr7:112122127-112122134 chr7:112122126-112122134 chr7:112122370-112122382 chr7:112122126-112122135 chr7:112122338-112122348
11	GATA2	chr7:112121849-112122260	HUVEC	blood vessel:	n/a	n/a
12	JUND	chr7:112121768-112122431	HCT-116	colon:	n/a	chr7:112122127-112122134 chr7:112122126-112122134 chr7:112122370-112122382 chr7:112122126-112122135 chr7:112122338-112122348
13	POLR2A	chr7:112121240-112122353	SK-N-SH	brain:	n/a	n/a
14	SMC3	chr7:112121841-112122318	Hela-S3	cervix:	n/a	n/a
15	TCF12	chr7:112121291-112122490	SK-N-SH	brain:	n/a	chr7:112122445-112122454
16	EP300	chr7:112121840-112122185	T-47D	breast:	n/a	chr7:112122125-112122134 chr7:112122126-112122135
17	STAT3	chr7:112121882-112122390	MCF10A-Er-Src	breast:	n/a	chr7:112122125-112122134 chr7:112122126-112122135
18	SRF	chr7:112121742-112122403	HCT-116	colon:	n/a	chr7:112122021-112122038 chr7:112122023-112122036
19	EP300	chr7:112121278-112122310	SK-N-SH_RA	brain:	n/a	chr7:112122125-112122134 chr7:112122126-112122135 chr7:112121586-112121595
20	FOS	chr7:112121874-112122327	MCF10A-Er-Src	breast:	n/a	chr7:112122127-112122134 chr7:112122126-112122134 chr7:112122126-112122135 chr7:112122124-112122135
21	GATA3	chr7:112121271-112122435	SK-N-SH	brain:	n/a	chr7:112121587-112121596
22	JUND	chr7:112121299-112122373	SK-N-SH	brain:	n/a	chr7:112122127-112122134 chr7:112122126-112122134 chr7:112122126-112122135 chr7:112122338-112122348 chr7:112121586-112121594 chr7:112121585-112121595 chr7:112121586-112121593
23	STAT3	chr7:112121794-112122276	MCF10A-Er-Src	breast:	n/a	chr7:112122125-112122134 chr7:112122126-112122135
24	MAX	chr7:112121685-112122406	A549	lung:	n/a	chr7:112122126-112122135 chr7:112122125-112122134
25	JUN	chr7:112121560-112122566	Hela-S3	cervix:	n/a	chr7:112122127-112122134 chr7:112122126-112122134 chr7:112122370-112122382 chr7:112122126-112122135 chr7:112122338-112122348 chr7:112121586-112121594 chr7:112121585-112121595 chr7:112121586-112121593
26	GATA3	chr7:112121618-112122425	A549	lung:	n/a	n/a
27	JUND	chr7:112121491-112122527	Hela-S3	cervix:	n/a	chr7:112122127-112122134 chr7:112122126-112122134 chr7:112122370-112122382 chr7:112122126-112122135 chr7:112122338-112122348 chr7:112121586-112121594 chr7:112121585-112121595 chr7:112121586-112121593
28	GATA3	chr7:112121779-112122269	T-47D	breast:	n/a	n/a
29	GATA3	chr7:112121704-112122432	MCF-7	breast:	n/a	n/a
30	TEAD4	chr7:112121336-112122270	SK-N-SH	brain:	n/a	n/a
31	EP300	chr7:112121714-112122359	MCF-7	breast:	n/a	chr7:112122125-112122134 chr7:112122126-112122135
32	EP300	chr7:112120254-112122906	SK-N-SH	brain:	n/a	chr7:112122125-112122134 chr7:112122126-112122135 chr7:112121586-112121595
33	PBX3	chr7:112121318-112122409	SK-N-SH	brain:	n/a	n/a
34	TCF12	chr7:112121398-112122521	SK-N-SH	brain:	n/a	chr7:112122445-112122454
35	MAX	chr7:112121872-112122206	K562	blood:	n/a	chr7:112122126-112122135 chr7:112122125-112122134
36	TCF12	chr7:112121831-112122362	MCF-7	breast:	n/a	n/a
37	JUND	chr7:112121713-112122534	SK-N-SH	brain:	n/a	chr7:112122127-112122134 chr7:112122126-112122134 chr7:112122370-112122382 chr7:112122126-112122135 chr7:112122338-112122348
38	GTF2F1	chr7:112121848-112122246	Hela-S3	cervix:	n/a	n/a
39	FOXA1	chr7:112121837-112122183	T-47D	breast:	n/a	n/a
40	TFAP2A	chr7:112121858-112122316	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr7:112121846-112122137	MCF-7	breast:	n/a	n/a
42	USF1	chr7:112121880-112122217	ECC-1	luminal epithelium:	n/a	n/a
43	TFAP2C	chr7:112121843-112122384	Hela-S3	cervix:	n/a	n/a
44	NFIC	chr7:112121486-112122484	SK-N-SH	brain:	n/a	n/a
45	GATA3	chr7:112121830-112122260	MCF-7	breast:	n/a	n/a
46	FOS	chr7:112121797-112122575	MCF10A-Er-Src	breast:	n/a	chr7:112122127-112122134 chr7:112122126-112122134 chr7:112122370-112122382 chr7:112122126-112122135 chr7:112122124-112122135 chr7:112122338-112122348
47	RAD21	chr7:112121880-112122288	Hela-S3	cervix:	n/a	n/a
48	USF1	chr7:112121794-112122404	HCT-116	colon:	n/a	n/a
49	JUND	chr7:112121682-112122386	MCF-7	breast:	n/a	chr7:112122127-112122134 chr7:112122126-112122134 chr7:112122370-112122382 chr7:112122126-112122135 chr7:112122338-112122348
50	RFX5	chr7:112121549-112122301	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:112089471..112094125-chr7:112120459..112123941,5	MCF-7	breast:
2	chr7:112121071..112126030-chr7:112126598..112131851,6	K562	blood:
3	chr7:112107719..112109774-chr7:112119889..112122320,2	K562	blood:
4	chr7:112088943..112098465-chr7:112111106..112127214,31	K562	blood:
5	chr7:112117720..112119517-chr7:112121271..112122829,2	K562	blood:
6	chr7:112121747..112122441-chr7:112135491..112136079,2	MCF-7	breast:
7	chr7:112121639..112123962-chr7:112132170..112134503,2	K562	blood:
8	chr7:112121406..112122230-chr7:112135636..112136388,2	MCF-7	breast:
9	chr7:112089441..112091037-chr7:112120327..112123054,3	MCF-7	breast:

Variant related genes	Relation type
LSMEM1	TF binding region
ENSG00000181016	Chromatin interaction
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1005659	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1005661	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024568	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1024569	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024570	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1024571	0.80[CEU][hapmap]
rs1024572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260414	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029631	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500007	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1054043	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953712	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10953713	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11514940	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764489	0.85[ASN][1000 genomes]
rs11769604	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12154294	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531101	0.86[ASN][1000 genomes]
rs12531636	0.86[ASN][1000 genomes]
rs1468457	1.00[ASN][1000 genomes]
rs1468458	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17159684	0.95[ASN][1000 genomes]
rs17159686	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1963308	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041066	0.81[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2041067	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2190587	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2396542	1.00[ASN][1000 genomes]
rs3095035	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3128384	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs34633971	1.00[ASN][1000 genomes]
rs36095669	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807206	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807210	1.00[ASN][1000 genomes]
rs3807213	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4275157	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4727771	0.91[ASN][1000 genomes]
rs4727774	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730548	0.91[ASN][1000 genomes]
rs4730549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs55954386	0.92[ASN][1000 genomes]
rs56020731	0.91[ASN][1000 genomes]
rs6944364	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6945176	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs6963343	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs6967593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6967894	0.92[ASN][1000 genomes]
rs6968084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6973615	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73201469	1.00[ASN][1000 genomes]
rs7455170	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777925	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7817	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv1030033	chr7:112092709-112140430	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12539263	IFRD1	cis	Thyroid	GTEx
rs12539263	IFRD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112100600-112135000	Weak transcription	Esophagus	oesophagus
2	chr7:112110600-112124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:112111200-112127200	Weak transcription	Fetal Brain Male	brain
4	chr7:112111600-112122200	Weak transcription	Fetal Kidney	kidney
5	chr7:112112400-112122200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:112112600-112129000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:112113200-112122600	Weak transcription	Colonic Mucosa	Colon
8	chr7:112113200-112124600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr7:112113200-112124800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:112113200-112125000	Weak transcription	Right Ventricle	heart
11	chr7:112113400-112127600	Weak transcription	Spleen	Spleen
12	chr7:112114400-112132000	Weak transcription	HepG2	liver
13	chr7:112114600-112125000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr7:112116400-112122000	Weak transcription	Fetal Lung	lung
15	chr7:112116600-112122000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:112116800-112132200	Weak transcription	Fetal Intestine Small	intestine
17	chr7:112117000-112122000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:112117000-112122200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:112117200-112125200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:112117200-112127200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:112117200-112128800	Weak transcription	Dnd41	blood
22	chr7:112117400-112122000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:112117400-112122000	Weak transcription	Adipose Nuclei	Adipose
24	chr7:112117400-112122400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:112117400-112124600	Weak transcription	Primary T cells from cord blood	blood
26	chr7:112117400-112124600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr7:112117400-112124800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr7:112117400-112130800	Weak transcription	Thymus	Thymus
29	chr7:112117600-112124800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:112117600-112125000	Weak transcription	Lung	lung
31	chr7:112117600-112125800	Weak transcription	Fetal Stomach	stomach
32	chr7:112117600-112131600	Weak transcription	Fetal Intestine Large	intestine
33	chr7:112117800-112122000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:112117800-112122000	Weak transcription	GM12878-XiMat	blood
35	chr7:112117800-112123200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr7:112118000-112122200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr7:112118000-112125000	Weak transcription	Placenta	Placenta
38	chr7:112118200-112124000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:112118200-112125000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:112118400-112122200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr7:112118800-112141600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:112119800-112122200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr7:112119800-112124800	Weak transcription	Fetal Thymus	thymus
44	chr7:112120200-112123000	Enhancers	Rectal Smooth Muscle	rectum
45	chr7:112120400-112122600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:112120400-112122600	Enhancers	HUVEC	blood vessel
47	chr7:112120400-112123000	Enhancers	NH-A	brain
48	chr7:112120600-112122600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:112120600-112122600	Enhancers	Brain Anterior Caudate	brain
50	chr7:112120600-112122600	Active TSS	Fetal Muscle Leg	muscle

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