Variant report

Variant	rs16869403
Chromosome Location	chr5:90356952-90356953
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90343505..90346725-chr5:90355686..90358630,4	MCF-7	breast:
2	chr5:90356230..90358804-chr5:90678069..90680261,3	K562	blood:
3	chr5:90356254..90357775-chr5:90359652..90362445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12109264	0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs16869404	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16869414	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs16869425	0.81[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1828177	1.00[YRI][hapmap]
rs1828178	1.00[YRI][hapmap]
rs1852731	0.81[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1858070	0.89[YRI][hapmap]
rs1876635	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1986718	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs2048217	0.90[YRI][hapmap]
rs2886924	0.90[CEU][hapmap]
rs2950849	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes]
rs2950850	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2950851	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs2950852	0.81[AMR][1000 genomes]
rs2950853	0.81[AMR][1000 genomes]
rs2950854	0.81[CEU][hapmap]
rs2950855	0.81[CEU][hapmap]
rs2973444	0.84[YRI][hapmap]
rs2973445	0.81[CEU][hapmap]
rs2973447	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs2973448	0.89[CEU][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes]
rs2973449	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs2973450	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs2973453	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs2973454	0.81[CEU][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2973455	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2973456	0.81[CEU][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3112484	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs3952745	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs56137437	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56377639	0.81[AMR][1000 genomes]
rs58524182	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59654682	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs59661306	0.83[EUR][1000 genomes]
rs66482530	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66608099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874106	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689544	1.00[YRI][hapmap]
rs73187140	0.91[ASN][1000 genomes]
rs73187144	0.91[ASN][1000 genomes]
rs73189008	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90341200-90376600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:90344800-90368000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:90349600-90358400	Weak transcription	Fetal Kidney	kidney
4	chr5:90352400-90367000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:90354200-90359600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:90354600-90358200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:90354600-90359000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:90354800-90368200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:90355200-90357200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:90355200-90358400	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:90355400-90357200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr5:90355400-90357400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr5:90355400-90357600	Weak transcription	Stomach Mucosa	stomach
14	chr5:90355400-90357600	Enhancers	GM12878-XiMat	blood
15	chr5:90355600-90357400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:90355600-90357800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:90356200-90357600	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links