Variant report

Variant	rs16893280
Chromosome Location	chr4:16292246-16292247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:16292192..16292811-chr4:16446518..16447107,2	MCF-7	breast:
2	chr4:16291654..16292299-chr4:16753545..16754247,2	MCF-7	breast:
3	chr4:16291175..16292655-chr4:16444905..16445780,4	MCF-7	breast:
4	chr4:16291216..16292322-chr4:16444840..16445760,4	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10489062	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11721872	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11731585	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11731731	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11733994	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11736183	0.86[ASN][1000 genomes]
rs1501130	0.83[ASN][1000 genomes]
rs1558451	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16893213	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16893226	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16893270	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16893307	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16893309	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16893310	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17308524	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1987772	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1987773	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2041538	0.86[ASN][1000 genomes]
rs2041539	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2109886	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2191955	0.85[ASN][1000 genomes]
rs2312942	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2312943	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2312945	0.88[ASN][1000 genomes]
rs28399788	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28608599	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34017372	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4066790	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41531449	0.86[ASN][1000 genomes]
rs4484297	0.95[EUR][1000 genomes]
rs4586928	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55823457	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56127222	0.84[ASN][1000 genomes]
rs57338172	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57499215	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59179944	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60333108	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60706134	0.93[EUR][1000 genomes]
rs61165707	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6449226	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6449227	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6449228	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6449229	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6449230	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6449232	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6449233	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6449234	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6449236	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67135076	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67412386	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67487480	0.86[ASN][1000 genomes]
rs67798922	0.91[EUR][1000 genomes]
rs67965240	0.86[ASN][1000 genomes]
rs6815201	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6821068	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6822072	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6826508	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6826788	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6834803	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6843493	0.87[AFR][1000 genomes]
rs6844050	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73234672	0.84[ASN][1000 genomes]
rs73234682	0.83[ASN][1000 genomes]
rs73234684	0.83[ASN][1000 genomes]
rs73235992	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7680027	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs7695368	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs929557	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs929558	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs975668	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs975669	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs975777	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs975778	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs990782	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv537048	chr4:16226406-16375787	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16291400-16293400	Enhancers	Fetal Kidney	kidney
2	chr4:16291600-16293200	Enhancers	Adipose Nuclei	Adipose
3	chr4:16291800-16292400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:16291800-16293000	Bivalent Enhancer	HUVEC	blood vessel
5	chr4:16291800-16293200	Enhancers	Fetal Brain Male	brain
6	chr4:16291800-16293400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr4:16292000-16292600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:16292000-16292600	Enhancers	Fetal Muscle Leg	muscle
9	chr4:16292000-16293000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:16292200-16292400	Enhancers	Osteobl	bone
11	chr4:16292200-16292600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:16292200-16292600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:16292200-16292600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:16292200-16292600	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr4:16292200-16292600	Enhancers	Stomach Mucosa	stomach
16	chr4:16292200-16293000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr4:16292200-16293800	Weak transcription	Fetal Stomach	stomach
18	chr4:16292200-16296000	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links