Variant report

Variant	rs712068
Chromosome Location	chr1:224713564-224713565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224690598..224692730-chr1:224711571..224713777,2	K562	blood:
2	chr1:224688210..224692730-chr1:224708810..224713777,4	K562	blood:
3	chr1:224711921..224714079-chr1:224715573..224717114,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10799582	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916635	0.93[EUR][1000 genomes]
rs10916636	0.93[EUR][1000 genomes]
rs10916637	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916638	0.83[EUR][1000 genomes]
rs10916639	0.90[EUR][1000 genomes]
rs10916640	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12033478	0.93[EUR][1000 genomes]
rs12043625	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12057775	0.91[CEU][hapmap];0.93[CHB][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12062991	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12068420	0.93[EUR][1000 genomes]
rs12072482	0.93[EUR][1000 genomes]
rs1317810	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1499283	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16849369	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2050625	0.93[EUR][1000 genomes]
rs2794804	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2794808	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4654047	0.93[EUR][1000 genomes]
rs61825839	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61825840	0.92[EUR][1000 genomes]
rs61825841	0.93[EUR][1000 genomes]
rs6656824	0.93[EUR][1000 genomes]
rs698277	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs698280	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712073	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712074	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs712075	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs712076	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs712082	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712084	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs712085	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712087	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712092	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7541415	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs791391	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs791393	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs791508	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs791509	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs791510	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs791511	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs791512	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs880368	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs983948	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs985301	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs989755	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs712068	LEFTY1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224694200-224717600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224694200-224727600	Weak transcription	Brain Anterior Caudate	brain
3	chr1:224696400-224716600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:224701800-224716600	Weak transcription	Ovary	ovary
5	chr1:224702000-224716600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:224702200-224716600	Weak transcription	Dnd41	blood
7	chr1:224705200-224713600	Weak transcription	Fetal Brain Male	brain
8	chr1:224709000-224714200	Enhancers	NHDF-Ad	bronchial
9	chr1:224710400-224713800	Enhancers	NH-A	brain
10	chr1:224710600-224716600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:224711200-224714000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:224711200-224720400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:224711400-224713800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:224711800-224713800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:224711800-224713800	Enhancers	Osteobl	bone
16	chr1:224711800-224716600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:224712000-224713600	Enhancers	HSMM	muscle
18	chr1:224712000-224713600	Enhancers	NHEK	skin
19	chr1:224712000-224730800	Weak transcription	Spleen	Spleen
20	chr1:224712200-224713800	Enhancers	NHLF	lung
21	chr1:224712800-224716600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:224713000-224716600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:224713200-224713800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:224713200-224716400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:224713200-224716600	Weak transcription	HSMMtube	muscle
26	chr1:224713400-224713800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:224713400-224716400	Weak transcription	HMEC	breast
28	chr1:224713400-224716600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:224713400-224721400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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