Variant report

Variant	rs11969304
Chromosome Location	chr6:28558636-28558637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28558273..28560922-chr6:28562703..28565525,2	K562	blood:
2	chr6:28558273..28560573-chr6:28562047..28564203,2	K562	blood:
3	chr6:28556555..28559076-chr6:28582763..28585041,2	K562	blood:
4	chr6:28558077..28560293-chr6:28570490..28573084,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPX5-1	chr6:28557006-28559524	XLOC_005223

Variant related genes	Relation type
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1015810	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962141	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11964748	0.91[EUR][1000 genomes]
rs11966042	1.00[CEU][hapmap]
rs11966949	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11968771	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970404	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078422	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108924	1.00[CEU][hapmap]
rs2159274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2531801	1.00[CEU][hapmap]
rs2531802	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2531816	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2531819	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531828	1.00[CEU][hapmap]
rs28382592	1.00[ASN][1000 genomes]
rs2859349	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859350	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859353	0.83[ASN][1000 genomes]
rs2859354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859367	1.00[CEU][hapmap]
rs2859371	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2859375	1.00[CEU][hapmap]
rs2859376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2859377	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2859378	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs385908	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400987	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403774	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423118	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57083092	0.91[EUR][1000 genomes]
rs57147168	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58025129	0.81[EUR][1000 genomes]
rs58945456	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59457415	1.00[ASN][1000 genomes]
rs60137363	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61540948	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923104	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs719370	1.00[CEU][hapmap]
rs73391136	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73391137	0.81[EUR][1000 genomes]
rs73391164	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73391166	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73391169	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73402995	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73403142	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403155	0.81[EUR][1000 genomes]
rs73403156	0.81[EUR][1000 genomes]
rs73403159	0.81[EUR][1000 genomes]
rs73403165	0.81[EUR][1000 genomes]
rs73403179	0.90[EUR][1000 genomes]
rs73404956	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73404986	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73405002	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73407126	1.00[ASN][1000 genomes]
rs73409118	0.86[ASN][1000 genomes]
rs73409123	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409134	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742658	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7751604	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28552400-28559600	Strong transcription	K562	blood
2	chr6:28557400-28559000	Enhancers	Pancreas	Pancrea
3	chr6:28558000-28565000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:28558200-28558800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:28558200-28558800	Bivalent/Poised TSS	Fetal Lung	lung
6	chr6:28558200-28558800	Enhancers	HepG2	liver
7	chr6:28558400-28558800	Enhancers	H9 Cell Line	embryonic stem cell
8	chr6:28558400-28558800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:28558400-28558800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:28558600-28558800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:28558600-28558800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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