Variant report

Variant	rs7545574
Chromosome Location	chr1:224879127-224879128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224854862..224857310-chr1:224877505..224879706,2	K562	blood:
2	chr1:224863910..224865687-chr1:224877704..224880301,2	K562	blood:
3	chr1:224877858..224879413-chr1:224882608..224884592,2	K562	blood:
4	chr1:224874942..224876608-chr1:224877645..224880078,2	K562	blood:
5	chr1:224869544..224871565-chr1:224877280..224879133,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10799277	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10799590	0.95[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs10915684	0.91[CEU][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs10915694	0.89[ASW][hapmap];0.87[CEU][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10915696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915698	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10915699	0.84[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12092438	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12121558	0.83[CEU][hapmap]
rs12124262	0.95[CEU][hapmap]
rs12130499	0.95[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs12132665	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs13374487	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1369847	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1436169	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1436171	0.84[CEU][hapmap];0.82[CHD][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1436172	1.00[CEU][hapmap]
rs1465768	0.84[CEU][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1603917	0.95[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs1603918	0.95[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs169888	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs1965777	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2405525	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2648746	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs2897161	0.80[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2936575	0.94[EUR][1000 genomes]
rs298732	0.94[EUR][1000 genomes]
rs298733	1.00[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs298734	0.94[EUR][1000 genomes]
rs298735	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs298738	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs298739	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2993124	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3012185	1.00[CEU][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4147293	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653402	1.00[CEU][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653404	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653591	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653592	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56881651	0.80[EUR][1000 genomes]
rs61676104	0.81[EUR][1000 genomes]
rs6667034	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6686604	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6686633	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67817586	0.90[EUR][1000 genomes]
rs713098	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs7511897	0.88[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7521396	0.90[EUR][1000 genomes]
rs7535296	0.95[CEU][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs7537973	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs7542431	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7542995	0.89[ASW][hapmap];0.87[CEU][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7543218	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544312	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs873594	0.84[CEU][hapmap];0.80[CHD][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7545574	RAB3GAP2	cis	cerebellum	SCAN
rs7545574	DEGS1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224832200-224884400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:224862400-224902000	Weak transcription	Pancreas	Pancrea
3	chr1:224871800-224884600	Weak transcription	Fetal Brain Female	brain
4	chr1:224873000-224884800	Weak transcription	NHLF	lung
5	chr1:224873400-224884200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:224875000-224881600	Weak transcription	NH-A	brain
7	chr1:224875200-224879400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:224875600-224888400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:224876200-224881200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:224876400-224881800	Weak transcription	NHDF-Ad	bronchial
11	chr1:224877400-224884000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:224877600-224891600	Weak transcription	Dnd41	blood
13	chr1:224877800-224880400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:224878400-224879400	Enhancers	HepG2	liver
15	chr1:224878800-224879600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:224878800-224880000	Enhancers	Ovary	ovary
17	chr1:224878800-224884200	Weak transcription	Fetal Brain Male	brain
18	chr1:224879000-224880000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:224879000-224884000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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