Variant report

Variant	rs1525554
Chromosome Location	chr7:3344017-3344018
allele	G/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	RAD21	chr7:3341429-3344236	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3340838..3343187-chr7:3343470..3345833,2	MCF-7	breast:
2	chr7:3342709..3344229-chr7:3346065..3349002,2	K562	blood:

Variant related genes	Relation type
ENSG00000236708	TF binding region
ENSG00000236708	Chromatin interaction
ENSG00000146555	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10499328	0.95[YRI][hapmap]
rs1522502	0.84[TSI][hapmap]
rs1525553	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133289	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs17133292	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.80[TSI][hapmap]
rs17133300	0.81[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.80[TSI][hapmap]
rs17133341	0.91[CEU][hapmap];0.80[YRI][hapmap];0.80[EUR][1000 genomes]
rs17133346	0.91[CEU][hapmap];0.82[CHB][hapmap];0.80[YRI][hapmap];0.83[EUR][1000 genomes]
rs17133355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[YRI][hapmap]
rs17133370	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs17133379	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs17133405	0.84[TSI][hapmap]
rs17133409	0.85[TSI][hapmap]
rs1880608	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2341582	0.83[EUR][1000 genomes]
rs28624198	0.83[ASN][1000 genomes]
rs28633216	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4326295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4343997	0.91[ASW][hapmap];0.91[CEU][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4418248	0.81[ASW][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap]
rs56142232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56143924	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56806161	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57893579	0.83[ASN][1000 genomes]
rs58608495	0.83[ASN][1000 genomes]
rs58713621	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59365175	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59604371	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59719823	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6462005	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66819701	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68100835	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6945059	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6950287	0.85[YRI][hapmap]
rs6955831	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6959573	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs6963701	1.00[CEU][hapmap]
rs6978143	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs73044757	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73044792	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73044797	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73046637	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73046678	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73046696	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73048618	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73288374	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73292178	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73672091	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73672093	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73675313	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7459157	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs7779576	0.91[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7780037	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7780894	0.93[YRI][hapmap]
rs7781736	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7788172	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7796564	1.00[CEU][hapmap]
rs7798732	0.82[CHB][hapmap]
rs7798784	0.85[ASN][1000 genomes]
rs7799163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7799969	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7801995	0.83[EUR][1000 genomes]
rs7807993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap]
rs7810155	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs7811986	0.82[AMR][1000 genomes]
rs9942558	1.00[CHB][hapmap]
rs9969312	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464264	chr7:3194156-3349625	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv605880	chr7:3194156-3349625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019515	chr7:3300048-3479972	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887324	chr7:3308195-3400105	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv605892	chr7:3341589-3424878	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1525554	SDK1	cis	Whole Blood	GTEx
rs1525554	FAM20C	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3342200-3344600	Weak transcription	Psoas Muscle	Psoas
2	chr7:3342600-3344200	Enhancers	Colon Smooth Muscle	Colon
3	chr7:3342600-3344600	Weak transcription	Fetal Brain Male	brain
4	chr7:3342600-3347200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:3342800-3345000	Weak transcription	Adipose Nuclei	Adipose
6	chr7:3343000-3345000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:3343600-3344600	Enhancers	Aorta	Aorta
8	chr7:3343800-3344600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:3343800-3357000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:3344000-3344200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:3344000-3344200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr7:3344000-3344200	Enhancers	Pancreas	Pancrea
13	chr7:3344000-3344200	Enhancers	Spleen	Spleen
14	chr7:3344000-3347000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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