Variant report

Variant	rs4077549
Chromosome Location	chr1:214679264-214679265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:214647353..214649494-chr1:214677849..214679754,2	MCF-7	breast:
2	chr1:214677645..214681280-chr1:214723322..214726744,5	MCF-7	breast:
3	chr1:214678638..214681169-chr1:214682598..214685287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152104	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10494981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588026	0.83[ASN][1000 genomes]
rs17023103	1.00[CEU][hapmap];0.93[AMR][1000 genomes]
rs17023144	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17023155	1.00[CHD][hapmap]
rs17734395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17734456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17734758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17734879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17734993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17791024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35329321	1.00[CHB][hapmap]
rs4074425	1.00[ASN][1000 genomes]
rs41307662	1.00[ASN][1000 genomes]
rs4448491	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529685	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535975	1.00[ASN][1000 genomes]
rs6540846	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs6540847	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs6540848	1.00[CEU][hapmap]
rs6662947	1.00[CEU][hapmap]
rs6675792	1.00[CHB][hapmap]
rs6698434	0.88[CEU][hapmap]
rs6701105	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6701315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs67542303	1.00[ASN][1000 genomes]
rs72759634	1.00[ASN][1000 genomes]
rs7521573	0.85[AFR][1000 genomes]
rs7550419	1.00[CHB][hapmap];1.00[JPT][hapmap];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	nsv468094	chr1:214654965-214687725	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv549180	chr1:214654965-214687725	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214665400-214705400	Weak transcription	Right Ventricle	heart
2	chr1:214668400-214680400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:214669800-214700400	Weak transcription	Aorta	Aorta
4	chr1:214670000-214680000	Weak transcription	NH-A	brain
5	chr1:214671800-214686800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:214674200-214685200	Weak transcription	HUVEC	blood vessel
7	chr1:214674200-214687200	Weak transcription	HSMMtube	muscle
8	chr1:214674400-214679400	Weak transcription	HMEC	breast
9	chr1:214674400-214680000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:214674400-214685000	Weak transcription	Fetal Stomach	stomach
11	chr1:214674600-214680000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:214674600-214680200	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:214674600-214686800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:214675000-214680000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:214675200-214680000	Weak transcription	NHDF-Ad	bronchial
16	chr1:214676000-214679800	Genic enhancers	NHEK	skin
17	chr1:214676400-214680000	Enhancers	A549	lung
18	chr1:214676600-214681000	Enhancers	Stomach Mucosa	stomach
19	chr1:214676800-214681400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:214677000-214680000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:214677000-214680000	Enhancers	HepG2	liver
22	chr1:214677000-214681600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:214677200-214679600	Strong transcription	HSMM	muscle
24	chr1:214677200-214690200	Weak transcription	Small Intestine	intestine
25	chr1:214677400-214679400	Enhancers	H9 Cell Line	embryonic stem cell
26	chr1:214677400-214679600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:214677400-214679600	Strong transcription	Osteobl	bone
28	chr1:214677400-214680200	Weak transcription	Hela-S3	cervix
29	chr1:214677600-214679400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:214677600-214679800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:214677600-214680800	Enhancers	Pancreas	Pancrea
32	chr1:214677800-214679600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:214677800-214679800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:214678000-214686800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:214678200-214680400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:214678200-214683400	Weak transcription	Gastric	stomach
37	chr1:214678200-214685400	Weak transcription	Esophagus	oesophagus
38	chr1:214678200-214687800	Weak transcription	Lung	lung
39	chr1:214678400-214679400	Weak transcription	Fetal Intestine Small	intestine
40	chr1:214678400-214681600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:214678600-214680800	Enhancers	Duodenum Mucosa	Duodenum
42	chr1:214678600-214680800	Enhancers	Placenta	Placenta
43	chr1:214678800-214679400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:214678800-214679600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:214678800-214679800	Weak transcription	Fetal Intestine Large	intestine
46	chr1:214678800-214680000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:214678800-214680000	Weak transcription	Left Ventricle	heart
48	chr1:214678800-214680200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:214678800-214680200	Weak transcription	Fetal Kidney	kidney
50	chr1:214679000-214679400	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links