Variant report

Variant	rs4656674
Chromosome Location	chr1:169370117-169370118
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1014965	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12119479	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12121891	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12124049	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12128350	0.86[EUR][1000 genomes]
rs12140572	0.84[EUR][1000 genomes]
rs12143708	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12730053	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12750775	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12758228	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17349579	0.85[EUR][1000 genomes]
rs17577184	0.91[EUR][1000 genomes]
rs35010461	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35107735	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656182	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4656671	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4656677	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4656678	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656680	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61806989	0.84[EUR][1000 genomes]
rs61807017	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6692649	0.86[EUR][1000 genomes]
rs722145	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7368145	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7527703	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7546347	0.85[AMR][1000 genomes];0.92[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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4656674	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169354800-169370600	Weak transcription	Fetal Kidney	kidney
2	chr1:169360600-169372200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:169360800-169370600	Weak transcription	NHLF	lung
4	chr1:169360800-169395200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:169362200-169371200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:169363400-169371200	Weak transcription	Ovary	ovary
7	chr1:169364400-169375600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:169365400-169370200	Weak transcription	NH-A	brain
9	chr1:169365600-169370800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:169365600-169371000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:169365600-169371200	Weak transcription	Fetal Lung	lung
12	chr1:169365800-169372400	Weak transcription	HSMM	muscle
13	chr1:169366000-169370400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:169367400-169370200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:169368200-169371000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:169369600-169370400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:169370000-169370400	ZNF genes & repeats	Brain Germinal Matrix	brain

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links