Variant report

Variant	rs1325821
Chromosome Location	chr6:53881312-53881313
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	MAFK	chr6:53881252-53881434	IMR90	lung:	n/a	n/a
2	MAFK	chr6:53881156-53881425	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL31-9	chr6:53881277-53881575	NONHSAT113209

Variant related genes	Relation type
MLIP	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1022931	0.90[JPT][hapmap]
rs10484651	0.85[JPT][hapmap]
rs10484652	0.90[JPT][hapmap]
rs10484653	0.90[JPT][hapmap]
rs10948793	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10948794	0.95[ASN][1000 genomes]
rs10948795	0.89[JPT][hapmap]
rs1156380	0.80[JPT][hapmap]
rs11961988	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12194304	0.85[JPT][hapmap]
rs12201302	0.85[JPT][hapmap]
rs12529752	0.95[ASN][1000 genomes]
rs12662586	1.00[ASW][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs13196004	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1409101	0.95[ASN][1000 genomes]
rs1570911	0.90[JPT][hapmap]
rs16884583	0.90[JPT][hapmap]
rs2397153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4715435	0.90[JPT][hapmap]
rs6914051	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6929778	0.93[ASN][1000 genomes]
rs9349691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370254	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9370255	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9370256	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382274	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395896	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9395899	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9395900	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1018062	chr6:53842588-53925192	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv5307	chr6:53874118-53952230	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr6:53875600-53883600	Weak transcription	Left Ventricle	heart
2	chr6:53876400-53883400	Weak transcription	Right Atrium	heart
3	chr6:53876600-53882200	Weak transcription	HSMM	muscle
4	chr6:53878200-53882600	Weak transcription	Liver	Liver
5	chr6:53879600-53883400	Weak transcription	Psoas Muscle	Psoas
6	chr6:53880200-53883200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:53880400-53882400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:53880600-53881400	Enhancers	Fetal Heart	heart
9	chr6:53880600-53882200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr6:53881200-53881600	Enhancers	Fetal Muscle Leg	muscle
11	chr6:53881200-53883400	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links