Variant report

Variant	rs651297
Chromosome Location	chr6:44260324-44260325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44258945..44261017-chr6:44295322..44296917,2	MCF-7	breast:
2	chr6:44223193..44226100-chr6:44259540..44261376,2	MCF-7	breast:
3	chr6:44213531..44216192-chr6:44260064..44261603,2	K562	blood:
4	chr6:44259968..44262335-chr6:44280810..44282440,2	MCF-7	breast:
5	chr6:44254194..44256325-chr6:44258837..44260906,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157593	Chromatin interaction
ENSG00000124608	Chromatin interaction
ENSG00000096384	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12215017	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1283567	0.81[ASN][1000 genomes]
rs12943	0.89[CEU][hapmap];0.83[GIH][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];0.80[YRI][hapmap]
rs167772	0.91[CHD][hapmap];0.81[JPT][hapmap]
rs2233437	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs324137	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs324138	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs324139	0.89[CEU][hapmap];0.83[GIH][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs324140	0.89[CEU][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs324142	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs324144	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs324145	0.89[CEU][hapmap];0.83[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs324146	0.89[CEU][hapmap];0.83[GIH][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs324147	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs325000	0.81[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs325001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs325002	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs325004	0.96[ASN][1000 genomes]
rs325007	0.83[ASW][hapmap]
rs325008	0.83[ASW][hapmap]
rs3799962	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs3818685	0.86[CHD][hapmap]
rs483536	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs498512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513688	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs516582	0.89[CEU][hapmap];0.83[GIH][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs557373	0.89[CEU][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs570469	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs614715	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs639728	0.93[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs694349	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs730775	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs7772949	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844315	0.82[AFR][1000 genomes];0.82[AMR][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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
7	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs651297	TCTE1	cis	cerebellum	SCAN
rs651297	ENPP5	cis	parietal	SCAN
rs651297	HSP90AB1	cis	cerebellum	SCAN
rs651297	PLA2G7	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44244400-44264800	Weak transcription	Right Atrium	heart
2	chr6:44257800-44260400	Enhancers	Fetal Brain Female	brain
3	chr6:44260000-44262600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links