Variant report

Variant	rs35400839
Chromosome Location	chr1:171743312-171743313
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171742868..171745559-chr1:171748625..171751508,3	MCF-7	breast:
2	chr1:171738743..171740462-chr1:171742324..171745005,2	K562	blood:
3	chr1:171710019..171713750-chr1:171741617..171744862,3	K562	blood:
4	chr1:171742778..171746827-chr1:171748449..171752347,7	K562	blood:

Variant related genes	Relation type
ENSG00000117533	Chromatin interaction
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1045456	0.99[EUR][1000 genomes]
rs10489252	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10913683	0.99[EUR][1000 genomes]
rs10913684	0.99[EUR][1000 genomes]
rs12091786	0.99[EUR][1000 genomes]
rs12565176	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12567851	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12730717	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12742601	1.00[EUR][1000 genomes]
rs12750330	0.88[EUR][1000 genomes]
rs12753043	0.99[EUR][1000 genomes]
rs17596025	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17596081	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649609	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17650310	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17650340	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17657363	0.91[EUR][1000 genomes]
rs1801898	0.99[EUR][1000 genomes]
rs2143369	0.99[EUR][1000 genomes]
rs2181216	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223602	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2232807	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2232813	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2232819	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2232824	0.99[EUR][1000 genomes]
rs2232825	0.88[EUR][1000 genomes]
rs236894	0.82[EUR][1000 genomes]
rs236897	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs236898	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs236899	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs236900	0.86[EUR][1000 genomes]
rs34320898	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34627492	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35249022	0.98[EUR][1000 genomes]
rs35631282	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35674909	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35882887	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35930163	0.99[EUR][1000 genomes]
rs36080557	0.99[EUR][1000 genomes]
rs3891278	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55732843	0.91[EUR][1000 genomes]
rs56365362	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56377810	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61807979	0.99[EUR][1000 genomes]
rs6656852	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6674364	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6675708	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6681322	0.99[EUR][1000 genomes]
rs6689125	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6695933	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7522582	0.99[EUR][1000 genomes]
rs7536142	0.99[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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35400839	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171739400-171744400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:171740000-171749800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links