Variant report

Variant	rs2520483
Chromosome Location	chr7:112062274-112062275
allele	C/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	CEBPB	chr7:112062005-112062591	HepG2	liver:	n/a	n/a
2	SPI1	chr7:112062182-112062383	K562	blood:	n/a	chr7:112062301-112062314 chr7:112062303-112062312 chr7:112062300-112062313
3	ELF1	chr7:112061779-112062540	K562	blood:	n/a	chr7:112062301-112062312
4	ELF1	chr7:112062126-112062504	HepG2	liver:	n/a	chr7:112062301-112062312
5	FOS	chr7:112061939-112062577	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr7:112061751-112062670	NB4	blood:	n/a	chr7:112062073-112062082
7	CTCF	chr7:112062220-112062370	A549	lung:	n/a	n/a
8	SPI1	chr7:112062013-112062607	HL-60	blood:	n/a	chr7:112062301-112062314 chr7:112062303-112062312 chr7:112062300-112062313
9	BACH1	chr7:112062140-112063468	H1-hESC	embryonic stem cell:	n/a	chr7:112063132-112063146
10	CEBPB	chr7:112061919-112062579	Hela-S3	cervix:	n/a	n/a
11	MAX	chr7:112061682-112062661	NB4	blood:	n/a	chr7:112062073-112062082
12	FOS	chr7:112061927-112063356	MCF10A-Er-Src	breast:	n/a	chr7:112063134-112063144 chr7:112063188-112063199 chr7:112063135-112063143 chr7:112063133-112063145 chr7:112063135-112063143 chr7:112063133-112063144 chr7:112063135-112063142
13	MAFK	chr7:112062190-112063382	H1-hESC	embryonic stem cell:	n/a	chr7:112063136-112063145 chr7:112063135-112063145 chr7:112063138-112063149 chr7:112063134-112063149 chr7:112063132-112063146
14	EP300	chr7:112062077-112063620	ECC-1	luminal epithelium:	n/a	chr7:112063135-112063144 chr7:112062303-112062312 chr7:112062404-112062418
15	ELF1	chr7:112062162-112062418	HepG2	liver:	n/a	chr7:112062301-112062312
16	JUND	chr7:112061945-112062424	H1-hESC	embryonic stem cell:	n/a	n/a
17	TCF7L2	chr7:112062059-112062545	Hela-S3	cervix:	n/a	chr7:112062355-112062371 chr7:112062358-112062367 chr7:112062357-112062367 chr7:112062359-112062368 chr7:112062360-112062367
18	FOXA2	chr7:112062267-112062512	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:112058693..112068099-chr7:112086961..112092875,22	MCF-7	breast:
2	chr7:112060910..112062508-chr7:112065563..112067389,2	K562	blood:
3	chr7:112058803..112077296-chr7:112087519..112096464,50	MCF-7	breast:
4	chr7:112060645..112065287-chr7:112088150..112093147,11	K562	blood:
5	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: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1015417	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1557698	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17492150	0.82[CHB][hapmap]
rs2396537	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2520468	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2520469	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2520472	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2520478	0.85[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2520479	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2520480	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2520481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2520484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523036	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523043	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708591	0.86[ASN][1000 genomes]
rs2708593	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708599	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36113101	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6977129	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs727807	1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs728273	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9640740	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs991632	0.98[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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112056800-112062400	Weak transcription	HUVEC	blood vessel
2	chr7:112059800-112064400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:112060200-112063200	Weak transcription	Fetal Heart	heart
4	chr7:112060400-112063000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr7:112060400-112063200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr7:112060600-112062800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr7:112060600-112064000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:112060800-112062600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:112060800-112064000	Enhancers	Brain Anterior Caudate	brain
10	chr7:112061000-112062400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:112061000-112063000	Weak transcription	HSMM	muscle
12	chr7:112061000-112063400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr7:112061000-112063600	Enhancers	Brain Angular Gyrus	brain
14	chr7:112061000-112063800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:112061000-112063800	Enhancers	Brain Cingulate Gyrus	brain
16	chr7:112061000-112063800	Enhancers	Brain Hippocampus Middle	brain
17	chr7:112061000-112063800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr7:112061000-112064000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:112061000-112064000	Enhancers	NHEK	skin
20	chr7:112061000-112064200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:112061000-112064400	Enhancers	HMEC	breast
22	chr7:112061000-112089800	Weak transcription	Aorta	Aorta
23	chr7:112061200-112062400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:112061200-112062600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:112061200-112062600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:112061200-112062600	Weak transcription	Colon Smooth Muscle	Colon
27	chr7:112061200-112062600	Weak transcription	Osteobl	bone
28	chr7:112061200-112062800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:112061200-112062800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:112061200-112063000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr7:112061200-112064400	Enhancers	Brain Substantia Nigra	brain
32	chr7:112061400-112062600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:112061400-112064400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:112061600-112062400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:112061600-112063400	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr7:112061600-112064000	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr7:112061600-112064000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr7:112061600-112065400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr7:112061800-112062400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:112061800-112062600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr7:112061800-112063000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr7:112061800-112063200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:112061800-112063200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:112061800-112063400	Enhancers	H9 Cell Line	embryonic stem cell
45	chr7:112061800-112063400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr7:112061800-112063400	Enhancers	Primary B cells from peripheral blood	blood
47	chr7:112061800-112063400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr7:112061800-112063400	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr7:112061800-112063600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr7:112061800-112063600	Enhancers	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links