Variant report

Variant	rs16869402
Chromosome Location	chr5:90355287-90355288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90353046..90355290-chr5:90674600..90676272,2	MCF-7	breast:
2	chr5:90354990..90356669-chr5:90674682..90677283,2	K562	blood:
3	chr5:90352115..90355751-chr5:90674816..90678609,4	MCF-7	breast:
4	chr5:90354607..90356691-chr5:90608614..90611398,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248323	Chromatin interaction
ENSG00000271762	Chromatin interaction
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10065773	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10076358	1.00[AMR][1000 genomes]
rs10077340	1.00[AMR][1000 genomes]
rs10080224	1.00[AMR][1000 genomes]
rs16869400	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16869424	1.00[EUR][1000 genomes]
rs16869431	1.00[EUR][1000 genomes]
rs16869437	1.00[EUR][1000 genomes]
rs16869489	1.00[EUR][1000 genomes]
rs59753442	1.00[EUR][1000 genomes]
rs6452943	1.00[EUR][1000 genomes]
rs6865161	1.00[AMR][1000 genomes]
rs6879069	1.00[EUR][1000 genomes]
rs6897191	1.00[EUR][1000 genomes]
rs7702079	1.00[EUR][1000 genomes]
rs7702715	1.00[EUR][1000 genomes]
rs7712139	1.00[EUR][1000 genomes]
rs7712353	1.00[EUR][1000 genomes]
rs7722301	1.00[EUR][1000 genomes]
rs7723655	1.00[EUR][1000 genomes]
rs7726939	1.00[EUR][1000 genomes]
rs7731268	1.00[EUR][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:21 , 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	chr5:90352800-90355600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr5:90353400-90355400	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr5:90353800-90355400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr5:90353800-90355400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:90353800-90355400	Enhancers	NHEK	skin
10	chr5:90354000-90355400	Enhancers	Stomach Mucosa	stomach
11	chr5:90354000-90355400	Enhancers	A549	lung
12	chr5:90354000-90355600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:90354200-90359600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:90354600-90355600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:90354600-90358200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:90354600-90359000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:90354800-90356000	Weak transcription	Lung	lung
18	chr5:90354800-90368200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:90355200-90355400	Flanking Active TSS	GM12878-XiMat	blood
20	chr5:90355200-90357200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:90355200-90358400	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links