Variant report

Variant	rs7988628
Chromosome Location	chr13:94474556-94474557
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:94474323..94476090-chr13:94476129..94477771,2	K562	blood:

Extended variants
information (count: 140 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10047752	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11617930	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12429919	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12876318	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1330468	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1411504	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411505	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411509	0.91[EUR][1000 genomes]
rs1411510	1.00[CEU][hapmap]
rs1411513	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1854730	0.92[EUR][1000 genomes]
rs1888230	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs1888231	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1888232	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1983987	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1983988	0.92[EUR][1000 genomes]
rs2008059	0.92[EUR][1000 genomes]
rs2150124	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2183426	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2183430	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2210110	0.87[EUR][1000 genomes]
rs2389048	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2892666	0.92[EUR][1000 genomes]
rs2892667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759422	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3759423	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3864992	0.92[EUR][1000 genomes]
rs3864993	0.92[EUR][1000 genomes]
rs3864994	0.92[EUR][1000 genomes]
rs4274304	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4274305	0.92[EUR][1000 genomes]
rs4300503	0.92[EUR][1000 genomes]
rs4486746	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4548731	0.92[EUR][1000 genomes]
rs4556669	0.92[EUR][1000 genomes]
rs6416428	0.92[EUR][1000 genomes]
rs71207435	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71207436	0.92[EUR][1000 genomes]
rs7317037	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7317144	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7320107	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7320571	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7326965	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7329113	0.91[EUR][1000 genomes]
rs7329264	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7330202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331637	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331870	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7490309	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7983205	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7986675	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7989528	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7991274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7998863	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001981	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs885192	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs928189	0.84[CEU][hapmap]
rs9284274	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9301910	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9301911	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9301912	0.95[EUR][1000 genomes]
rs9301913	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9301914	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs9301916	0.95[CEU][hapmap]
rs9516286	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9516287	0.92[EUR][1000 genomes]
rs9516289	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9516290	0.82[EUR][1000 genomes]
rs9516295	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516296	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516297	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516301	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs9516302	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs9516306	0.82[EUR][1000 genomes]
rs9524190	0.95[CEU][hapmap]
rs9524212	0.91[EUR][1000 genomes]
rs9524214	0.92[EUR][1000 genomes]
rs9524215	0.91[EUR][1000 genomes]
rs9524216	0.92[EUR][1000 genomes]
rs9524217	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9524218	0.92[EUR][1000 genomes]
rs9524222	0.92[EUR][1000 genomes]
rs9524223	0.92[EUR][1000 genomes]
rs9524224	0.92[EUR][1000 genomes]
rs9524225	0.92[EUR][1000 genomes]
rs9524226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524229	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524231	0.92[EUR][1000 genomes]
rs9524232	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524235	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524236	0.92[EUR][1000 genomes]
rs9524237	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524243	0.96[EUR][1000 genomes]
rs9524247	0.95[EUR][1000 genomes]
rs9524249	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9524252	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524253	0.84[EUR][1000 genomes]
rs9524254	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9524256	0.80[CEU][hapmap]
rs9524257	0.83[EUR][1000 genomes]
rs9524263	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9524264	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs9524265	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs9524268	0.95[CEU][hapmap]
rs9556324	0.91[EUR][1000 genomes]
rs9556325	0.91[EUR][1000 genomes]
rs9556326	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9556327	0.89[EUR][1000 genomes]
rs9556328	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9556334	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9561444	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9561445	0.91[EUR][1000 genomes]
rs9561447	0.92[EUR][1000 genomes]
rs9561448	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9561449	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9561453	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561458	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9589836	0.92[EUR][1000 genomes]
rs9589837	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9589841	0.95[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9589842	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9589848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs991431	0.83[EUR][1000 genomes]
rs991596	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs991597	0.90[EUR][1000 genomes]
rs996920	0.81[EUR][1000 genomes]
rs996921	1.00[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv934193	chr13:94462018-94493268	Weak transcription Enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7988628	GPC6	cis	Artery Aorta	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94461200-94483200	Weak transcription	Fetal Intestine Small	intestine
2	chr13:94467200-94477000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr13:94467400-94476800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:94471000-94475600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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