Variant report

Variant	rs59977708
Chromosome Location	chr1:77857899-77857900
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17098286	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851266	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59295145	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72679564	0.96[EUR][1000 genomes]
rs72679591	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72679594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59977708	PIGK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77845200-77860000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:77845200-77878000	Weak transcription	Primary T cells from cord blood	blood
3	chr1:77845200-77878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:77846400-77859200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:77847400-77860200	Weak transcription	HSMM	muscle
6	chr1:77848400-77859400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:77854000-77865200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:77854200-77860200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:77854200-77863600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:77854200-77864200	Weak transcription	Brain Germinal Matrix	brain
11	chr1:77854800-77858000	Weak transcription	Osteobl	bone
12	chr1:77854800-77859600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:77854800-77860000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:77854800-77862600	Weak transcription	Aorta	Aorta
15	chr1:77855000-77859200	Weak transcription	NHDF-Ad	bronchial
16	chr1:77855000-77859800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:77855000-77860000	Weak transcription	NHLF	lung
18	chr1:77855000-77863800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:77856000-77858400	Enhancers	Brain Angular Gyrus	brain
20	chr1:77856000-77858400	Enhancers	Brain Substantia Nigra	brain
21	chr1:77856200-77858400	Enhancers	Brain Hippocampus Middle	brain
22	chr1:77856600-77858000	Enhancers	Brain Cingulate Gyrus	brain
23	chr1:77857000-77859400	Weak transcription	Brain Anterior Caudate	brain
24	chr1:77857400-77858200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr1:77857800-77859000	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links