Variant report

Variant	rs6834488
Chromosome Location	chr4:88178919-88178920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88177898..88180525-chr4:88185534..88188362,3	K562	blood:

Variant related genes	Relation type
ENSG00000250572	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10000324	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10001545	0.95[ASN][1000 genomes]
rs10022237	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10084835	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs10433879	0.86[ASN][1000 genomes]
rs10433937	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10440365	0.89[ASN][1000 genomes]
rs11727374	0.91[ASN][1000 genomes]
rs11735092	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11935592	0.95[ASN][1000 genomes]
rs13108668	0.81[YRI][hapmap]
rs13130041	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13130929	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13140105	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13142110	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13142655	0.99[ASN][1000 genomes]
rs13150068	0.93[ASN][1000 genomes]
rs13150834	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs28418877	0.95[ASN][1000 genomes]
rs28419230	0.94[ASN][1000 genomes]
rs28439498	0.93[ASN][1000 genomes]
rs28456144	0.88[ASN][1000 genomes]
rs28528308	0.89[ASN][1000 genomes]
rs28636836	0.81[ASN][1000 genomes]
rs28657030	0.89[ASN][1000 genomes]
rs28664118	0.95[ASN][1000 genomes]
rs28679728	0.95[ASN][1000 genomes]
rs3923442	0.81[YRI][hapmap]
rs4089	0.88[ASN][1000 genomes]
rs4583723	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4998663	0.95[ASN][1000 genomes]
rs6531965	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6531967	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6816742	0.81[YRI][hapmap]
rs6850131	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6850509	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7656630	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7663544	0.81[ASN][1000 genomes]
rs7684895	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7688657	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7694379	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7699556	0.81[YRI][hapmap]

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	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1014846	chr4:88151614-88188335	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537170	chr4:88151614-88188335	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv516203	chr4:88167878-88228228	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88177200-88179600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:88178000-88179000	Enhancers	Brain Hippocampus Middle	brain
3	chr4:88178000-88179800	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr4:88178200-88179600	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr4:88178200-88180000	Enhancers	Brain Anterior Caudate	brain
6	chr4:88178600-88179400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:88178800-88179200	Flanking Active TSS	Brain Substantia Nigra	brain
8	chr4:88178800-88179400	Weak transcription	Brain Cingulate Gyrus	brain

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