Variant report

Variant	rs2389049
Chromosome Location	chr13:94462100-94462101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12876221	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1330461	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330462	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330466	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs1330467	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1360300	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411501	0.82[ASW][hapmap];0.96[CEU][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1411506	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411511	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17195813	0.90[CEU][hapmap]
rs1854731	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs2150125	0.83[ASW][hapmap];0.91[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2183427	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2183429	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389050	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272893	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4337169	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4366594	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4389020	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4517643	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4558277	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4773761	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs61964368	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6492680	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492681	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71203705	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7324433	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326722	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7328659	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7330375	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7337988	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7983687	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7993741	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7995215	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7995578	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8001985	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8002684	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs913942	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301908	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9516292	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524210	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524211	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524246	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524260	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524273	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9556335	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9589863	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs991432	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs991595	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][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
rs2389049	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	chr13:94461800-94462200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:94461800-94463800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr13:94461800-94464000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:94461800-94464200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr13:94461800-94464200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:94462000-94462200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr13:94462000-94462200	Enhancers	Ovary	ovary
18	chr13:94462000-94462600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr13:94462000-94464000	Enhancers	H1 Cell Line	embryonic stem cell

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