Variant report

Variant	rs1405716
Chromosome Location	chr2:178500799-178500800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178497999..178500939-chr2:178626259..178628565,2	K562	blood:
2	chr2:178499231..178501761-chr2:178503904..178506555,2	K562	blood:
3	chr2:178196424..178198872-chr2:178498721..178501636,2	K562	blood:
4	chr2:178480859..178483355-chr2:178499342..178501117,2	K562	blood:
5	chr2:178500261..178502540-chr2:178503904..178505684,2	K562	blood:
6	chr2:178490562..178493751-chr2:178498705..178503907,5	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10189303	1.00[JPT][hapmap]
rs10469714	1.00[JPT][hapmap]
rs10497493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680632	0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12618150	0.96[YRI][hapmap]
rs12618542	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs12619506	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13000926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010396	1.00[JPT][hapmap]
rs13014512	0.84[EUR][1000 genomes]
rs13017429	0.96[YRI][hapmap]
rs13019660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13025391	1.00[ASW][hapmap];0.84[LWK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs13025904	1.00[ASW][hapmap];0.84[LWK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs13026012	0.81[AFR][1000 genomes]
rs13028757	1.00[ASW][hapmap];0.84[LWK][hapmap];0.93[YRI][hapmap]
rs13034781	0.81[LWK][hapmap]
rs13034886	1.00[JPT][hapmap]
rs1358326	0.93[ASW][hapmap];0.96[YRI][hapmap]
rs1358327	0.96[YRI][hapmap]
rs1527398	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1527399	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]
rs1527400	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1527402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527410	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1534304	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs1544001	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs1544003	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1547580	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1547581	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1547582	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16865535	0.85[CHD][hapmap]
rs1997206	0.96[YRI][hapmap]
rs1997208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293471	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs2365619	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs2365620	0.93[YRI][hapmap]
rs2886422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731802	1.00[JPT][hapmap]
rs3770003	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4110134	0.93[YRI][hapmap]
rs4341975	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs4893972	1.00[JPT][hapmap]
rs4893974	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4893975	0.93[ASW][hapmap];0.84[CEU][hapmap];0.95[CHD][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893976	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893977	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433683	0.97[EUR][1000 genomes]
rs6433685	0.93[YRI][hapmap]
rs6433687	0.93[ASW][hapmap];0.92[YRI][hapmap]
rs6705405	1.00[JPT][hapmap]
rs6721360	0.96[YRI][hapmap]
rs6730406	0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs6734426	0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs6734683	1.00[JPT][hapmap]
rs7422544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560080	0.96[YRI][hapmap]
rs7560514	0.96[YRI][hapmap]
rs7560737	0.93[ASW][hapmap];0.96[YRI][hapmap]
rs7577174	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7578901	0.96[YRI][hapmap]
rs7586934	0.93[ASW][hapmap];0.96[YRI][hapmap]
rs7591796	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7591897	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7594290	0.85[CHD][hapmap]
rs7597640	0.96[YRI][hapmap]
rs941271	0.96[YRI][hapmap]
rs941276	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1405716	AGPS	cis	cerebellum	SCAN
rs1405716	TTC30B	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178499200-178503400	Weak transcription	Fetal Muscle Leg	muscle
2	chr2:178499200-178503600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:178499200-178505400	Weak transcription	Fetal Lung	lung
4	chr2:178499800-178504000	Weak transcription	Right Atrium	heart
5	chr2:178499800-178505400	Weak transcription	Fetal Kidney	kidney
6	chr2:178500000-178501000	Enhancers	GM12878-XiMat	blood
7	chr2:178500000-178501600	Weak transcription	K562	blood
8	chr2:178500000-178502200	Enhancers	Dnd41	blood
9	chr2:178500000-178503600	Weak transcription	Fetal Brain Male	brain
10	chr2:178500000-178504400	Weak transcription	Fetal Brain Female	brain
11	chr2:178500200-178505600	Weak transcription	Left Ventricle	heart

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