Variant report

Variant	rs609946
Chromosome Location	chr6:4074146-4074147
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4073171..4075702-chr6:4076261..4078769,2	K562	blood:
2	chr6:4073031..4076036-chr6:4129401..4132460,3	K562	blood:
3	chr6:4067254..4070253-chr6:4071525..4075483,4	K562	blood:

Variant related genes	Relation type
ENSG00000252668	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs101418	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11755877	0.93[ASN][1000 genomes]
rs1204951	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2326408	0.84[ASN][1000 genomes]
rs2473597	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745453	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745455	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2783063	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2783073	0.84[ASN][1000 genomes]
rs584585	0.84[ASN][1000 genomes]
rs588158	0.87[ASN][1000 genomes]
rs589494	0.85[ASN][1000 genomes]
rs590675	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592953	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593291	0.99[ASN][1000 genomes]
rs594662	1.00[ASN][1000 genomes]
rs595413	1.00[ASN][1000 genomes]
rs608195	0.91[ASN][1000 genomes]
rs611500	0.84[ASN][1000 genomes]
rs612022	0.84[ASN][1000 genomes]
rs612477	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs613028	0.86[ASN][1000 genomes]
rs613260	0.84[ASN][1000 genomes]
rs613709	0.84[ASN][1000 genomes]
rs617604	0.93[ASN][1000 genomes]
rs617790	0.84[ASN][1000 genomes]
rs619439	0.84[ASN][1000 genomes]
rs619483	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs619873	0.84[ASN][1000 genomes]
rs620484	0.84[ASN][1000 genomes]
rs620901	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs626080	0.86[ASN][1000 genomes]
rs627259	0.91[ASN][1000 genomes]
rs629362	0.84[ASN][1000 genomes]
rs633290	0.84[ASN][1000 genomes]
rs634114	0.93[ASN][1000 genomes]
rs634698	0.84[ASN][1000 genomes]
rs639905	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643232	0.84[ASN][1000 genomes]
rs648900	0.84[ASN][1000 genomes]
rs649725	0.84[ASN][1000 genomes]
rs650183	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs651246	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653431	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654621	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654982	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659025	0.84[ASN][1000 genomes]
rs659305	0.84[ASN][1000 genomes]
rs660560	0.84[ASN][1000 genomes]
rs661404	0.84[ASN][1000 genomes]
rs661657	0.92[ASN][1000 genomes]
rs662834	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs664299	0.82[ASN][1000 genomes]
rs664839	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs665728	0.93[ASN][1000 genomes]
rs665894	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs666254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs668070	0.88[ASN][1000 genomes]
rs670932	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671364	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674543	0.89[ASN][1000 genomes]
rs676683	0.84[ASN][1000 genomes]
rs682063	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs688176	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689308	0.84[ASN][1000 genomes]
rs694903	0.91[ASN][1000 genomes]
rs707991	0.89[ASN][1000 genomes]
rs7166	0.84[ASN][1000 genomes]
rs7744628	0.84[ASN][1000 genomes]
rs7756630	0.89[ASN][1000 genomes]
rs7757606	0.84[ASN][1000 genomes]
rs853416	0.84[ASN][1000 genomes]
rs853417	0.84[ASN][1000 genomes]
rs9328220	0.84[ASN][1000 genomes]
rs9378395	0.99[ASN][1000 genomes]
rs9405219	0.93[ASN][1000 genomes]
rs942475	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4058200-4075000	Weak transcription	Small Intestine	intestine
2	chr6:4063400-4078800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:4064000-4077600	Weak transcription	Brain Anterior Caudate	brain
4	chr6:4065200-4077400	Weak transcription	Brain Substantia Nigra	brain
5	chr6:4066000-4077400	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:4066200-4077400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:4066400-4077200	Weak transcription	Adipose Nuclei	Adipose
8	chr6:4066400-4077400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:4066600-4077400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:4066800-4079600	Weak transcription	NHLF	lung
11	chr6:4067000-4082400	Weak transcription	Brain Germinal Matrix	brain
12	chr6:4068600-4074800	Weak transcription	HepG2	liver
13	chr6:4071800-4075200	Weak transcription	Stomach Mucosa	stomach
14	chr6:4073800-4077600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:4074000-4074400	Enhancers	Pancreas	Pancrea

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