Variant report

Variant	rs2235454
Chromosome Location	chr1:209778439-209778440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209751620..209753341-chr1:209777265..209778868,2	MCF-7	breast:
2	chr1:209778292..209780941-chr1:209782673..209784930,2	K562	blood:
3	chr1:209776929..209778715-chr1:209779809..209782231,2	K562	blood:

Variant related genes	Relation type
ENSG00000008118	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11119313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801272	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12079523	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12402938	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408760	0.84[EUR][1000 genomes]
rs12734177	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235449	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235452	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235453	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235455	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34741019	0.80[EUR][1000 genomes]
rs35104617	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35458333	0.80[EUR][1000 genomes]
rs35498535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35503098	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35508847	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35553417	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35856006	0.80[EUR][1000 genomes]
rs55814069	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74157978	0.92[ASN][1000 genomes]
rs74157980	0.92[ASN][1000 genomes]
rs7517804	0.87[EUR][1000 genomes]
rs7517839	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553120	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760833	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9787069	0.81[EUR][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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209764200-209780400	Weak transcription	Fetal Brain Male	brain
2	chr1:209764600-209791200	Weak transcription	Brain Anterior Caudate	brain
3	chr1:209769800-209781000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:209769800-209781200	Weak transcription	Spleen	Spleen
5	chr1:209771000-209780600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:209771000-209787600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:209772200-209783000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:209774200-209780400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:209774800-209780400	Weak transcription	HMEC	breast
10	chr1:209775600-209791400	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:209775800-209780200	Weak transcription	NHEK	skin
12	chr1:209775800-209780400	Weak transcription	Osteobl	bone
13	chr1:209775800-209789800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:209776000-209790200	Weak transcription	Brain Germinal Matrix	brain
15	chr1:209776000-209791000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:209776400-209780000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:209776800-209781200	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr1:209777600-209779600	Weak transcription	Fetal Lung	lung
19	chr1:209777800-209793000	Weak transcription	Ovary	ovary
20	chr1:209777800-209796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:209778200-209779000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:209778400-209778800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr1:209778400-209780200	Weak transcription	Fetal Heart	heart
24	chr1:209778400-209791400	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links