Variant report

Variant	rs28594984
Chromosome Location	chr7:112060730-112060731
allele	C/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	FOXA1	chr7:112060174-112060771	T-47D	breast:	n/a	n/a
2	MAX	chr7:112060100-112061054	ECC-1	luminal epithelium:	n/a	chr7:112060324-112060337 chr7:112060326-112060335 chr7:112060324-112060337 chr7:112060325-112060334 chr7:112060325-112060335 chr7:112060327-112060334 chr7:112060325-112060336 chr7:112060326-112060336 chr7:112060326-112060335 chr7:112060326-112060336 chr7:112060325-112060336
3	GATA3	chr7:112060301-112060827	T-47D	breast:	n/a	chr7:112060312-112060319
4	FOXA1	chr7:112060256-112060766	T-47D	breast:	n/a	n/a
5	TCF12	chr7:112060197-112061017	ECC-1	luminal epithelium:	n/a	chr7:112060775-112060785
6	CEBPB	chr7:112060311-112060839	ECC-1	luminal epithelium:	n/a	chr7:112060414-112060425
7	MYC	chr7:112060195-112061025	MCF10A-Er-Src	breast:	n/a	chr7:112060324-112060337 chr7:112060326-112060335 chr7:112060324-112060337 chr7:112060325-112060334 chr7:112060325-112060335 chr7:112060327-112060334 chr7:112060325-112060336 chr7:112060326-112060336 chr7:112060326-112060335 chr7:112060326-112060336 chr7:112060325-112060336
8	NFIC	chr7:112060241-112061115	ECC-1	luminal epithelium:	n/a	n/a
9	TEAD4	chr7:112060172-112061110	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr7:112060161-112061128	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr7:112060590-112060770	MCF10A-Er-Src	breast:	n/a	n/a
12	EP300	chr7:112060353-112060855	T-47D	breast:	n/a	n/a
13	TCF12	chr7:112060201-112061054	ECC-1	luminal epithelium:	n/a	chr7:112060775-112060785
14	TEAD4	chr7:112060236-112061063	ECC-1	luminal epithelium:	n/a	n/a
15	MAX	chr7:112060232-112061061	ECC-1	luminal epithelium:	n/a	chr7:112060324-112060337 chr7:112060326-112060335 chr7:112060324-112060337 chr7:112060325-112060334 chr7:112060325-112060335 chr7:112060327-112060334 chr7:112060325-112060336 chr7:112060326-112060336 chr7:112060326-112060335 chr7:112060326-112060336 chr7:112060325-112060336
16	EP300	chr7:112060214-112061158	ECC-1	luminal epithelium:	n/a	n/a
17	FOXM1	chr7:112060189-112060947	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:112058693..112068099-chr7:112086961..112092875,22	MCF-7	breast:
2	chr7:112055161..112057071-chr7:112058715..112061690,2	MCF-7	breast:
3	chr7:112054145..112057717-chr7:112058317..112061377,3	K562	blood:
4	chr7:112058803..112077296-chr7:112087519..112096464,50	MCF-7	breast:
5	chr7:112060645..112065287-chr7:112088150..112093147,11	K562	blood:
6	chr7:112060641..112062150-chr7:112065491..112067917,2	K562	blood:
7	chr7:112059129..112067568-chr7:112088387..112093703,18	K562	blood:

Variant related genes	Relation type
IFRD1	TF binding region
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1007587	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1014725	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215841	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225540	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226613	1.00[ASN][1000 genomes]
rs10227934	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229525	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229822	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229978	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10230608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10232364	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10232380	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10234035	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10234996	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235364	1.00[EUR][1000 genomes]
rs10238838	1.00[EUR][1000 genomes]
rs10238839	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10239076	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10244575	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247540	1.00[ASN][1000 genomes]
rs10248735	1.00[ASN][1000 genomes]
rs10248923	1.00[EUR][1000 genomes]
rs10249330	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249953	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10251712	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252768	1.00[EUR][1000 genomes]
rs10253360	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254160	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10257492	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10257831	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10257850	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258413	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259763	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10262723	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10263624	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264118	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264797	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266828	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10269074	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270151	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10273461	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275709	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10276062	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10276695	1.00[EUR][1000 genomes]
rs10276868	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10276907	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277444	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10278528	1.00[EUR][1000 genomes]
rs10278642	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10278883	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279631	1.00[ASN][1000 genomes]
rs10280408	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487289	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12333548	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437769	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437855	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13438058	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13438257	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159423	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159431	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159432	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159440	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159444	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159475	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159496	1.00[ASN][1000 genomes]
rs17159531	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159613	1.00[ASN][1000 genomes]
rs17159615	1.00[ASN][1000 genomes]
rs1989940	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040726	1.00[EUR][1000 genomes]
rs2214434	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396525	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396534	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396535	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729540	1.00[ASN][1000 genomes]
rs28402908	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28407071	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28490504	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28516940	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28563007	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28566952	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602472	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654705	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712358	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718033	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28797808	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321927	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392819	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727767	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727768	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727769	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730514	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730515	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730521	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730523	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730525	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730526	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730527	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730528	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730530	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730531	1.00[ASN][1000 genomes]
rs4730534	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730535	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730537	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730538	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730545	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57771476	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58514081	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60046006	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60317474	1.00[ASN][1000 genomes]
rs60677549	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948649	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950339	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950367	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954131	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965959	0.87[EUR][1000 genomes]
rs6973251	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975374	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977315	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726422	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73424453	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783041	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886351	1.00[ASN][1000 genomes]
rs886352	1.00[ASN][1000 genomes]
rs9986709	0.80[AMR][1000 genomes];1.00[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	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112051600-112062000	Weak transcription	Right Atrium	heart
2	chr7:112053800-112062000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr7:112056400-112061800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:112056400-112061800	Weak transcription	Thymus	Thymus
5	chr7:112056600-112061800	Weak transcription	Fetal Thymus	thymus
6	chr7:112056800-112062400	Weak transcription	HUVEC	blood vessel
7	chr7:112057000-112061600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:112057200-112061600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:112057400-112061200	Weak transcription	Dnd41	blood
10	chr7:112059400-112061800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:112059800-112060800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr7:112059800-112061000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:112059800-112061200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:112059800-112061800	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr7:112059800-112064400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:112060000-112061800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr7:112060000-112062000	Weak transcription	Esophagus	oesophagus
18	chr7:112060200-112061000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:112060200-112061000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:112060200-112061000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:112060200-112061000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:112060200-112061000	Flanking Active TSS	NHEK	skin
23	chr7:112060200-112063200	Weak transcription	Fetal Heart	heart
24	chr7:112060400-112060800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr7:112060400-112060800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:112060400-112060800	Enhancers	Primary hematopoietic stem cells	blood
27	chr7:112060400-112060800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:112060400-112060800	Active TSS	Brain Anterior Caudate	brain
29	chr7:112060400-112060800	Enhancers	Brain Germinal Matrix	brain
30	chr7:112060400-112060800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr7:112060400-112060800	Flanking Active TSS	HepG2	liver
32	chr7:112060400-112061000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:112060400-112061000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr7:112060400-112061000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:112060400-112061000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr7:112060400-112061000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:112060400-112061000	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr7:112060400-112061000	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr7:112060400-112061000	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr7:112060400-112061000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr7:112060400-112061000	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr7:112060400-112061000	Flanking Active TSS	HMEC	breast
43	chr7:112060400-112061000	Flanking Active TSS	Osteobl	bone
44	chr7:112060400-112061200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr7:112060400-112061200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr7:112060400-112061200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:112060400-112061200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:112060400-112061200	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr7:112060400-112061200	Flanking Active TSS	NHDF-Ad	bronchial
50	chr7:112060400-112061400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links