Variant report

Variant	rs6666455
Chromosome Location	chr1:179339415-179339416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:179338705..179340694-chr1:179346963..179349066,2	K562	blood:
2	chr1:179089949..179090868-chr1:179338641..179339706,4	K562	blood:
3	chr1:179332952..179336574-chr1:179337996..179342859,7	MCF-7	breast:
4	chr1:179048422..179049068-chr1:179338591..179339827,3	K562	blood:
5	chr1:179220558..179221464-chr1:179338599..179339569,5	MCF-7	breast:
6	chr1:179220394..179221467-chr1:179338651..179339953,9	MCF-7	breast:
7	chr1:179333390..179336673-chr1:179338029..179341473,3	MCF-7	breast:
8	chr1:179338659..179339560-chr1:179568499..179569458,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000263633	Chromatin interaction
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10494517	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs10494518	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs10798674	0.84[MKK][hapmap]
rs10913736	0.80[GIH][hapmap]
rs11581470	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs11585517	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs11808258	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs13306732	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16854042	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17369088	0.86[GIH][hapmap]
rs2209922	0.81[JPT][hapmap]
rs2274622	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2296960	0.87[CEU][hapmap]
rs4072451	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4072452	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4111171	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs4651024	0.91[GIH][hapmap]
rs4651029	0.85[ASN][1000 genomes]
rs4652366	0.84[GIH][hapmap]
rs4652367	0.87[CHB][hapmap]
rs4652369	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4652380	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs4652406	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4652412	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs56232973	0.93[EUR][1000 genomes]
rs56275144	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59559400	0.85[ASN][1000 genomes]
rs6425538	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6425557	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs6425574	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs6665787	0.97[EUR][1000 genomes]
rs6668120	0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs6674086	0.87[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs6679542	0.81[JPT][hapmap]
rs6700149	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs7413415	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs7512638	0.87[CEU][hapmap]
rs7520806	0.87[CEU][hapmap]
rs7521291	0.85[ASN][1000 genomes]
rs7529227	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs964983	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs964984	0.87[CEU][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv33901	chr1:179328708-179344905	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6666455	TDRD5	cis	cerebellum	SCAN
rs6666455	TDRD5	cis	Artery Tibial	GTEx
rs6666455	TDRD5	cis	Thyroid	GTEx
rs6666455	RASAL2	cis	parietal	SCAN
rs6666455	RP11-545A16.3	cis	Artery Aorta	GTEx
rs6666455	TDRD5	cis	Artery Aorta	GTEx
rs6666455	TDRD5	cis	Adipose Subcutaneous	GTEx
rs6666455	AXDND1	cis	Thyroid	GTEx
rs6666455	TDRD5	cis	Esophagus Mucosa	GTEx
rs6666455	TDRD5	cis	lung	GTEx
rs6666455	TDRD5	cis	parietal	SCAN
rs6666455	TDRD5	cis	Nerve Tibial	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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