Variant report

Variant	rs3765978
Chromosome Location	chr1:86893325-86893326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86892715..86895192-chr1:86898265..86899891,2	K562	blood:
2	chr1:86890838..86893158-chr1:86893303..86895296,2	MCF-7	breast:
3	chr1:86891052..86893486-chr1:86893692..86895662,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10493789	0.87[ASN][1000 genomes]
rs10747328	0.84[ASN][1000 genomes]
rs11161820	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1158505	0.87[ASN][1000 genomes]
rs12564227	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1334143	0.87[ASN][1000 genomes]
rs1334146	0.84[ASN][1000 genomes]
rs1334147	0.87[ASN][1000 genomes]
rs1334148	0.85[ASN][1000 genomes]
rs1334150	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17129055	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17129078	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1931363	0.85[ASN][1000 genomes]
rs2104963	0.84[ASN][1000 genomes]
rs2151708	0.85[ASN][1000 genomes]
rs2151709	0.87[ASN][1000 genomes]
rs2249296	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2250857	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2252313	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2791464	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3765975	0.87[ASN][1000 genomes]
rs4292929	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61800656	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61804060	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs883200	0.85[ASN][1000 genomes]
rs9433030	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9787365	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[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	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86882200-86894800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:86887200-86895000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:86888000-86894800	Weak transcription	NHDF-Ad	bronchial
4	chr1:86888200-86894600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:86889400-86894400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:86889800-86895200	Weak transcription	Psoas Muscle	Psoas
7	chr1:86890200-86895200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:86890400-86895000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:86890600-86894600	Weak transcription	Osteobl	bone
10	chr1:86890600-86894800	Weak transcription	Adipose Nuclei	Adipose
11	chr1:86890600-86903000	Weak transcription	Esophagus	oesophagus
12	chr1:86890800-86894400	Weak transcription	Hela-S3	cervix
13	chr1:86890800-86894600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:86890800-86894600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:86891600-86894800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:86892000-86894400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:86893000-86894000	Weak transcription	HMEC	breast
18	chr1:86893000-86894400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:86893000-86894600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:86893000-86894600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:86893000-86894800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:86893000-86895200	Genic enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links