Variant report

Variant	rs3130351
Chromosome Location	chr6:30328192-30328193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr6:30328089-30328303	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30293903..30295934-chr6:30327520..30329116,2	MCF-7	breast:
2	chr6:30312350..30314370-chr6:30326387..30329065,2	MCF-7	breast:

Variant related genes	Relation type
HCG19P	TF binding region
ENSG00000231074	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000270604	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11158	0.81[EUR][1000 genomes]
rs2106072	0.81[EUR][1000 genomes]
rs2157678	0.80[EUR][1000 genomes]
rs2517609	0.88[EUR][1000 genomes]
rs2517617	0.88[EUR][1000 genomes]
rs2517622	0.81[EUR][1000 genomes]
rs2523712	0.88[EUR][1000 genomes]
rs2523729	0.81[EUR][1000 genomes]
rs2844777	0.91[EUR][1000 genomes]
rs3094034	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3094036	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3094054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094064	0.98[EUR][1000 genomes]
rs3094066	0.95[EUR][1000 genomes]
rs3094067	0.98[EUR][1000 genomes]
rs3094069	0.95[EUR][1000 genomes]
rs3094078	0.95[EUR][1000 genomes]
rs3094620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094621	0.89[EUR][1000 genomes]
rs3094622	0.89[EUR][1000 genomes]
rs3094624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094628	0.90[EUR][1000 genomes]
rs3129815	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3129830	0.95[EUR][1000 genomes]
rs3130350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130355	0.98[EUR][1000 genomes]
rs3130363	0.86[EUR][1000 genomes]
rs3130364	1.00[EUR][1000 genomes]
rs3130377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130380	0.95[EUR][1000 genomes]
rs3130399	0.95[EUR][1000 genomes]
rs3132647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs3130351	HLA-C	cis	multi-tissue	Pritchard
rs3130351	HLA-A	cis	brain	seeQTL
rs3130351	TRIM40	cis	multi-tissue	Pritchard
rs3130351	HLA-G	cis	multi-tissue	Pritchard
rs3130351	XM_173626	trans	multi-tissue	Pritchard
rs3130351	HLA-H	cis	multi-tissue	Pritchard
rs3130351	HLA-DQA1	cis	multi-tissue	Pritchard
rs3130351	HLA-A	cis	multi-tissue	Pritchard
rs3130351	ZFP57	cis	multi-tissue	Pritchard
rs3130351	HLA-A	trans	brain	seeQTL
rs3130351	HLA-DRB1	cis	multi-tissue	Pritchard
rs3130351	C6orf12	cis	multi-tissue	Pritchard
rs3130351	BTN3A2	cis	multi-tissue	Pritchard
rs3130351	HLA-DQB1	cis	multi-tissue	Pritchard
rs3130351	Contig14433_RC	trans	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30326400-30331200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:30327800-30328400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr6:30328000-30328200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:30328000-30328200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:30328000-30328200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr6:30328000-30328400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links