Variant report

Variant	rs1411504
Chromosome Location	chr13:94462330-94462331
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10047752	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10775112	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11617930	0.96[EUR][1000 genomes]
rs12429919	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12876318	0.96[EUR][1000 genomes]
rs1330468	0.82[EUR][1000 genomes]
rs1411505	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411507	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411509	0.93[EUR][1000 genomes]
rs1411513	0.90[EUR][1000 genomes]
rs1854730	0.96[EUR][1000 genomes]
rs1888230	0.82[EUR][1000 genomes]
rs1888231	0.84[EUR][1000 genomes]
rs1888232	0.84[EUR][1000 genomes]
rs1983987	0.86[EUR][1000 genomes]
rs1983988	0.92[EUR][1000 genomes]
rs2008059	0.96[EUR][1000 genomes]
rs2150124	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183426	0.96[EUR][1000 genomes]
rs2183430	0.92[EUR][1000 genomes]
rs2210110	0.87[EUR][1000 genomes]
rs2389048	0.84[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	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759422	0.96[EUR][1000 genomes]
rs3759423	0.96[EUR][1000 genomes]
rs3864992	0.96[EUR][1000 genomes]
rs3864993	0.96[EUR][1000 genomes]
rs3864994	0.96[EUR][1000 genomes]
rs4274304	0.96[EUR][1000 genomes]
rs4274305	0.96[EUR][1000 genomes]
rs4300503	0.96[EUR][1000 genomes]
rs4486746	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	0.92[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	0.94[EUR][1000 genomes]
rs7317144	0.96[EUR][1000 genomes]
rs7320107	0.88[EUR][1000 genomes]
rs7320571	0.96[EUR][1000 genomes]
rs7326965	0.84[EUR][1000 genomes]
rs7329113	0.95[EUR][1000 genomes]
rs7329264	0.84[EUR][1000 genomes]
rs7330202	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7331637	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7331870	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7490309	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7983205	0.86[EUR][1000 genomes]
rs7986675	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7988628	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7991274	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7998863	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7999251	0.91[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	0.95[EUR][1000 genomes]
rs9284274	0.87[EUR][1000 genomes]
rs9301910	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9301911	0.86[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	0.85[EUR][1000 genomes]
rs9301914	0.82[EUR][1000 genomes]
rs9516286	0.92[EUR][1000 genomes]
rs9516287	0.96[EUR][1000 genomes]
rs9516289	0.96[EUR][1000 genomes]
rs9516290	0.86[EUR][1000 genomes]
rs9516295	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516296	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516297	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516301	0.82[EUR][1000 genomes]
rs9516302	0.82[EUR][1000 genomes]
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	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	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524227	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524228	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524229	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524230	0.83[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	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524235	0.88[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	0.93[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	0.91[EUR][1000 genomes]
rs9524252	0.85[EUR][1000 genomes]
rs9524253	0.83[EUR][1000 genomes]
rs9524254	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9524257	0.82[EUR][1000 genomes]
rs9524263	0.88[EUR][1000 genomes]
rs9524264	0.80[EUR][1000 genomes]
rs9524265	0.80[EUR][1000 genomes]
rs9556324	0.95[EUR][1000 genomes]
rs9556325	0.95[EUR][1000 genomes]
rs9556326	0.95[EUR][1000 genomes]
rs9556327	0.93[EUR][1000 genomes]
rs9556328	0.96[EUR][1000 genomes]
rs9556334	0.87[EUR][1000 genomes]
rs9561444	0.95[EUR][1000 genomes]
rs9561445	0.95[EUR][1000 genomes]
rs9561447	0.96[EUR][1000 genomes]
rs9561448	0.96[EUR][1000 genomes]
rs9561449	0.96[EUR][1000 genomes]
rs9561453	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9561458	0.90[EUR][1000 genomes]
rs9589836	0.96[EUR][1000 genomes]
rs9589837	0.96[EUR][1000 genomes]
rs9589841	0.90[EUR][1000 genomes]
rs9589842	0.96[EUR][1000 genomes]
rs9589848	0.85[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	0.82[EUR][1000 genomes]
rs991597	0.90[EUR][1000 genomes]
rs996920	0.80[EUR][1000 genomes]
rs996921	0.88[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
rs1411504	GPC6	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94450200-94464200	Weak transcription	HSMM	muscle
2	chr13:94458400-94462600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:94460000-94462400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr13:94460000-94463200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:94461000-94463000	Enhancers	H9 Cell Line	embryonic stem cell
6	chr13:94461000-94464000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr13:94461000-94464800	Enhancers	Fetal Heart	heart
8	chr13:94461200-94483200	Weak transcription	Fetal Intestine Small	intestine
9	chr13:94461400-94464200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr13:94461400-94464200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr13:94461800-94463800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr13:94461800-94464000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:94461800-94464200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr13:94461800-94464200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:94462000-94462600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr13:94462000-94464000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr13:94462200-94462600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:94462200-94463000	Enhancers	HepG2	liver
19	chr13:94462200-94463400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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