Variant report

Variant	rs9524228
Chromosome Location	chr13:94458222-94458223
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10047752	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10775112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11617930	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12429919	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12876318	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1330468	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs1411504	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411505	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411509	0.93[EUR][1000 genomes]
rs1411510	1.00[CEU][hapmap]
rs1411513	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1854730	0.96[EUR][1000 genomes]
rs1888230	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1888231	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1888232	0.84[EUR][1000 genomes]
rs1983987	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs1983988	0.92[EUR][1000 genomes]
rs2008059	0.96[EUR][1000 genomes]
rs2150124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183426	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2183430	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2210110	0.87[EUR][1000 genomes]
rs2389048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892666	0.96[EUR][1000 genomes]
rs2892667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759422	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3759423	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3864992	0.96[EUR][1000 genomes]
rs3864993	0.96[EUR][1000 genomes]
rs3864994	0.96[EUR][1000 genomes]
rs4274304	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4274305	0.96[EUR][1000 genomes]
rs4300503	0.96[EUR][1000 genomes]
rs4486746	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4548731	0.96[EUR][1000 genomes]
rs4556669	0.96[EUR][1000 genomes]
rs4556670	0.82[EUR][1000 genomes]
rs6416428	0.96[EUR][1000 genomes]
rs71207435	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71207436	0.96[EUR][1000 genomes]
rs7317037	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7317144	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7320107	0.88[EUR][1000 genomes]
rs7320571	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7326965	0.84[EUR][1000 genomes]
rs7329113	0.95[EUR][1000 genomes]
rs7329264	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7330202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7331637	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7331870	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7490309	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7983205	0.86[EUR][1000 genomes]
rs7986675	0.90[EUR][1000 genomes]
rs7988628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7989528	0.92[CEU][hapmap]
rs7991274	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7998863	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7999251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8001981	0.84[EUR][1000 genomes]
rs885192	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs928189	0.83[CEU][hapmap]
rs9284274	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs9301910	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9301911	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9301912	0.94[EUR][1000 genomes]
rs9301913	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs9301914	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs9301916	0.92[CEU][hapmap]
rs9516286	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9516287	0.96[EUR][1000 genomes]
rs9516289	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9516290	0.86[EUR][1000 genomes]
rs9516295	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516296	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516297	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516301	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs9516302	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs9524190	0.84[CEU][hapmap]
rs9524212	0.95[EUR][1000 genomes]
rs9524214	0.96[EUR][1000 genomes]
rs9524215	0.95[EUR][1000 genomes]
rs9524216	0.96[EUR][1000 genomes]
rs9524217	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9524218	0.96[EUR][1000 genomes]
rs9524222	0.96[EUR][1000 genomes]
rs9524223	0.96[EUR][1000 genomes]
rs9524224	0.96[EUR][1000 genomes]
rs9524225	0.96[EUR][1000 genomes]
rs9524226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524229	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524231	0.96[EUR][1000 genomes]
rs9524232	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524235	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524236	0.96[EUR][1000 genomes]
rs9524237	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524243	0.95[EUR][1000 genomes]
rs9524247	0.94[EUR][1000 genomes]
rs9524249	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9524252	0.85[EUR][1000 genomes]
rs9524253	0.83[EUR][1000 genomes]
rs9524254	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs9524257	0.82[EUR][1000 genomes]
rs9524263	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9524264	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs9524265	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs9524268	0.92[CEU][hapmap]
rs9556324	0.95[EUR][1000 genomes]
rs9556325	0.95[EUR][1000 genomes]
rs9556326	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9556327	0.93[EUR][1000 genomes]
rs9556328	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9556334	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9561444	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9561445	0.95[EUR][1000 genomes]
rs9561447	0.96[EUR][1000 genomes]
rs9561448	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9561449	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9561453	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9561458	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9589836	0.96[EUR][1000 genomes]
rs9589837	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9589841	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs9589842	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9589848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs991431	0.82[EUR][1000 genomes]
rs991596	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs991597	0.90[EUR][1000 genomes]
rs996920	0.80[EUR][1000 genomes]
rs996921	1.00[CEU][hapmap];0.88[EUR][1000 genomes]

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	nsv948714	chr13:94100104-94699435	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv933807	chr13:94187158-94845505	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1045230	chr13:94277683-94764671	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv832684	chr13:94379507-94550853	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv948455	chr13:94451368-94988900	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9524228	GPC6	cis	Artery Aorta	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94450200-94464200	Weak transcription	HSMM	muscle
2	chr13:94452200-94462000	Weak transcription	Ovary	ovary
3	chr13:94457800-94460200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr13:94458000-94458600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr13:94458200-94458400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:94458200-94460200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr13:94458200-94461000	Weak transcription	H9 Cell Line	embryonic stem cell

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