Variant report

Variant	rs28471674
Chromosome Location	chr9:98174980-98174981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98171235..98175849-chr9:98186797..98190089,10	MCF-7	breast:
2	chr9:98173705..98177734-chr9:98187506..98190870,3	MCF-7	breast:
3	chr9:98172979..98174989-chr9:98178552..98180377,2	MCF-7	breast:
4	chr9:98173730..98177988-chr9:98187520..98191004,5	K562	blood:
5	chr9:98174491..98183187-chr9:98187141..98190074,10	K562	blood:

Variant related genes	Relation type
ENSG00000237857	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10821464	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10993529	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10993534	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12004780	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2036514	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2404693	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28679639	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35041950	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35402806	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35431736	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs357521	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs357522	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs357552	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59710018	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62558314	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479605	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7388704	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7868504	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs905615	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs913711	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9695482	0.94[AMR][1000 genomes];0.85[EUR][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	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1051731	chr9:98154815-98201115	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98160400-98188400	Weak transcription	Pancreas	Pancrea
2	chr9:98169800-98183600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:98169800-98183800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr9:98172800-98176000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:98172800-98183600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:98173000-98175000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:98173000-98176000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:98173000-98177600	Weak transcription	NHLF	lung
9	chr9:98173000-98181200	Weak transcription	NHEK	skin
10	chr9:98173000-98183600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:98173200-98176000	Weak transcription	A549	lung
12	chr9:98173200-98183400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:98173200-98184000	Weak transcription	Fetal Intestine Large	intestine
14	chr9:98173400-98184000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:98173600-98175400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:98173600-98188200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:98173800-98184000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:98174000-98183800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:98174200-98175200	Enhancers	K562	blood
20	chr9:98174200-98183400	Weak transcription	Fetal Intestine Small	intestine
21	chr9:98174200-98183800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:98174400-98175400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:98174600-98175200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:98174600-98175200	Weak transcription	Fetal Stomach	stomach
25	chr9:98174600-98176400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:98174600-98182800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:98174800-98177800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links