Variant report

Variant	rs6540846
Chromosome Location	chr1:214683657-214683658
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:214679463..214680976-chr1:214683287..214685488,2	K562	blood:
2	chr1:214678638..214681169-chr1:214682598..214685287,2	MCF-7	breast:
3	chr1:214648053..214650360-chr1:214683258..214686104,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10494981	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs11588026	0.83[ASN][1000 genomes]
rs17023144	1.00[MEX][hapmap];0.93[TSI][hapmap]
rs17023155	1.00[CHD][hapmap]
rs17734395	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17734456	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17734758	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs17734879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17734993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17791024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35329321	1.00[CHB][hapmap];0.85[TSI][hapmap]
rs4074425	1.00[ASN][1000 genomes]
rs4077549	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]
rs41307662	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4448491	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529685	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535975	1.00[ASN][1000 genomes]
rs6540847	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs6675792	1.00[CHB][hapmap]
rs6701105	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6701315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67542303	1.00[ASN][1000 genomes]
rs72759634	1.00[ASN][1000 genomes]
rs7550419	0.82[CEU][hapmap];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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214665400-214705400	Weak transcription	Right Ventricle	heart
2	chr1:214669800-214700400	Weak transcription	Aorta	Aorta
3	chr1:214671800-214686800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:214674200-214685200	Weak transcription	HUVEC	blood vessel
5	chr1:214674200-214687200	Weak transcription	HSMMtube	muscle
6	chr1:214674400-214685000	Weak transcription	Fetal Stomach	stomach
7	chr1:214674600-214686800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:214677200-214690200	Weak transcription	Small Intestine	intestine
9	chr1:214678000-214686800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:214678200-214685400	Weak transcription	Esophagus	oesophagus
11	chr1:214678200-214687800	Weak transcription	Lung	lung
12	chr1:214679000-214684000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:214679000-214687400	Weak transcription	Ovary	ovary
14	chr1:214679200-214687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:214679600-214687600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:214680200-214685400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:214680800-214684200	Weak transcription	Psoas Muscle	Psoas
18	chr1:214680800-214686800	Weak transcription	HSMM	muscle
19	chr1:214680800-214687600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:214680800-214687600	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:214680800-214687800	Weak transcription	Left Ventricle	heart
22	chr1:214681000-214685400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:214681000-214686600	Weak transcription	NH-A	brain
24	chr1:214681000-214687200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:214681000-214688000	Weak transcription	Hela-S3	cervix
26	chr1:214681200-214688200	Weak transcription	Fetal Kidney	kidney
27	chr1:214681400-214684600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:214681400-214686800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:214681600-214684200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:214681600-214690200	Weak transcription	Pancreas	Pancrea
31	chr1:214681800-214685800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr1:214681800-214686000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:214682000-214683800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:214682000-214684400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:214682000-214685800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:214682400-214685200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr1:214682600-214684200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr1:214682800-214684400	Strong transcription	Osteobl	bone
39	chr1:214683400-214683800	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:214683400-214683800	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
41	chr1:214683400-214683800	Enhancers	Gastric	stomach
42	chr1:214683400-214683800	ZNF genes & repeats	A549	lung
43	chr1:214683400-214684200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:214683400-214684200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr1:214683400-214684200	ZNF genes & repeats	HMEC	breast
46	chr1:214683400-214684200	Strong transcription	NHEK	skin
47	chr1:214683400-214684400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
48	chr1:214683400-214685200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:214683600-214684000	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
50	chr1:214683600-214684400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links