Variant report

Variant	rs7540074
Chromosome Location	chr1:184360262-184360263
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	POLR2A	chr1:184359879-184360368	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr1:184360039-184360444	MCF10A-Er-Src	breast:	n/a	n/a
3	KAP1	chr1:184360008-184360726	U2OS	brain:	n/a	chr1:184360464-184360472
4	POLR2A	chr1:184359942-184360428	SK-N-MC	brain:	n/a	n/a
5	FOS	chr1:184360111-184360694	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr1:184359893-184360523	MCF-7	breast:	n/a	chr1:184360286-184360297 chr1:184360285-184360296
7	CEBPB	chr1:184359999-184360450	A549	lung:	n/a	chr1:184360286-184360297 chr1:184360285-184360296
8	CEBPB	chr1:184359979-184360359	K562	blood:	n/a	chr1:184360286-184360297 chr1:184360285-184360296
9	CEBPB	chr1:184360047-184360425	MCF-7	breast:	n/a	chr1:184360286-184360297 chr1:184360285-184360296
10	E2F4	chr1:184359965-184360434	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr1:184360132-184360638	MCF10A-Er-Src	breast:	n/a	n/a
12	TCF7L2	chr1:184360012-184360736	HEK293	kidney:	n/a	n/a
13	CEBPB	chr1:184360014-184360385	HepG2	liver:	n/a	chr1:184360286-184360297 chr1:184360285-184360296
14	MYC	chr1:184360119-184360721	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr1:184359935-184360455	IMR90	lung:	n/a	chr1:184360286-184360297 chr1:184360285-184360296
16	FOS	chr1:184360028-184360692	MCF10A-Er-Src	breast:	n/a	n/a
17	FOXP2	chr1:184360034-184360449	SK-N-MC	brain:	n/a	n/a
18	FOXP2	chr1:184360223-184360376	SK-N-MC	brain:	n/a	n/a
19	FOS	chr1:184360176-184360445	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr1:184360155-184360454	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:184360163-184360461	MCF10A-Er-Src	breast:	n/a	n/a
22	CEBPB	chr1:184360236-184360436	Hela-S3	cervix:	n/a	chr1:184360286-184360297 chr1:184360285-184360296

No.	Distal block	Cell Line	Cell type
1	chr1:184358940..184362912-chr1:184372683..184376846,4	MCF-7	breast:
2	chr1:184359142..184361251-chr1:184383132..184386323,3	MCF-7	breast:
3	chr1:184021075..184023141-chr1:184357467..184360640,3	MCF-7	breast:
4	chr1:184355826..184357579-chr1:184359686..184361272,2	K562	blood:

Variant related genes	Relation type
ENSG00000271387	TF binding region
ENSG00000116667	Chromatin interaction
ENSG00000271387	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs16823065	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16823118	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16823145	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2207524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2378842	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3814334	1.00[CHB][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3922451	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57590305	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58863963	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59158738	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59237100	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59598210	0.93[ASN][1000 genomes]
rs60066136	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6424951	1.00[EUR][1000 genomes]
rs6659461	0.91[ASN][1000 genomes]
rs6683308	0.80[AFR][1000 genomes]
rs6695258	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6698504	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs73061677	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73061691	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73063504	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73063508	0.81[ASN][1000 genomes]
rs73063512	0.81[ASN][1000 genomes]
rs73063527	0.81[ASN][1000 genomes]
rs7525041	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7550032	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv3821	chr1:184319543-184365236	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184357400-184362000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:184357400-184362200	Weak transcription	Gastric	stomach
3	chr1:184357600-184360600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:184357600-184362000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:184357800-184362000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:184357800-184362200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:184358000-184360400	Weak transcription	Placenta	Placenta
8	chr1:184358000-184362200	Weak transcription	Lung	lung
9	chr1:184358000-184373400	Weak transcription	Ovary	ovary
10	chr1:184358200-184360600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:184358200-184361000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:184358200-184372200	Weak transcription	Fetal Kidney	kidney
13	chr1:184358200-184374000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:184358400-184360600	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:184358400-184360600	Enhancers	Fetal Brain Male	brain
16	chr1:184358400-184360800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:184358400-184362000	Weak transcription	Esophagus	oesophagus
18	chr1:184358400-184362800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:184358400-184364400	Enhancers	HMEC	breast
20	chr1:184358400-184378200	Weak transcription	Brain Angular Gyrus	brain
21	chr1:184358600-184360600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr1:184358600-184363600	Weak transcription	Adipose Nuclei	Adipose
23	chr1:184358800-184361200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr1:184358800-184361400	Weak transcription	Right Ventricle	heart
25	chr1:184359000-184360400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:184359000-184360600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:184359000-184360600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr1:184359000-184368600	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:184359000-184382800	Weak transcription	Fetal Stomach	stomach
30	chr1:184359200-184361800	Weak transcription	Small Intestine	intestine
31	chr1:184359200-184363000	Weak transcription	Osteobl	bone
32	chr1:184359400-184360400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:184359400-184362000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:184359400-184362200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:184359400-184362600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:184359400-184362800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:184359400-184377000	Weak transcription	Fetal Intestine Small	intestine
38	chr1:184359600-184360400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:184359600-184360400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:184359600-184360400	Weak transcription	Brain Germinal Matrix	brain
41	chr1:184359600-184360600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr1:184359600-184360600	Enhancers	Fetal Brain Female	brain
43	chr1:184359600-184360600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:184359600-184361000	Weak transcription	Left Ventricle	heart
45	chr1:184359600-184361400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:184359600-184361400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:184359600-184361400	Weak transcription	Right Atrium	heart
48	chr1:184359600-184362400	Enhancers	NHEK	skin
49	chr1:184359600-184362800	Enhancers	Psoas Muscle	Psoas
50	chr1:184359600-184363400	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links