Variant report

Variant	rs6746233
Chromosome Location	chr2:178472535-178472536
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178468577..178471398-chr2:178471772..178474287,2	K562	blood:
2	chr2:178470776..178473144-chr6:142522946..142525040,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10201367	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10201883	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10497497	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10497499	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930802	0.83[ASN][1000 genomes]
rs11679519	0.85[CEU][hapmap]
rs11679730	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs11680632	1.00[CHB][hapmap]
rs11694013	0.87[EUR][1000 genomes]
rs11694988	0.85[CEU][hapmap]
rs12618150	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12620285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12988366	0.83[CEU][hapmap]
rs13017234	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs13017429	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs13025391	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs13025904	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs13026012	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs13028757	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1317945	0.83[EUR][1000 genomes]
rs13431105	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1358326	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1358327	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1446839	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527403	0.90[EUR][1000 genomes]
rs1534305	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1544001	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1852530	0.85[CEU][hapmap]
rs1918345	0.91[EUR][1000 genomes]
rs1918347	0.82[EUR][1000 genomes]
rs1997206	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1997207	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs2091442	0.90[EUR][1000 genomes]
rs2222712	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs2365620	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2365621	0.83[EUR][1000 genomes]
rs2695315	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4110134	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs4341975	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs4893967	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4893970	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4893973	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4893978	0.83[EUR][1000 genomes]
rs5025340	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs57986285	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58160847	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6433685	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6433686	0.82[EUR][1000 genomes]
rs6433687	0.83[EUR][1000 genomes]
rs6433688	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6721360	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6723031	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6723063	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6755382	0.81[EUR][1000 genomes]
rs6756918	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7560080	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7560514	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7560737	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7573345	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs7577552	0.83[EUR][1000 genomes]
rs7578901	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7582179	0.84[CEU][hapmap]
rs7586934	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7593744	1.00[CHB][hapmap]
rs7593753	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7597640	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs941271	1.00[CHB][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2762964	chr2:178416394-178481818	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3506731	chr2:178416851-178482200	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3506732	chr2:178416851-178482200	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3520312	chr2:178417102-178482200	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3520313	chr2:178417102-178482200	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	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
9	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6746233	AGPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178462800-178475600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:178462800-178482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:178463800-178475400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:178464200-178482600	Weak transcription	Psoas Muscle	Psoas
5	chr2:178464200-178482600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:178464600-178482400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:178468400-178482800	Weak transcription	Fetal Brain Male	brain
8	chr2:178469400-178475000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:178469400-178475000	Weak transcription	Aorta	Aorta
10	chr2:178471600-178472600	Enhancers	Fetal Kidney	kidney
11	chr2:178471800-178473200	Weak transcription	HepG2	liver
12	chr2:178471800-178475600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:178471800-178477400	Weak transcription	Fetal Stomach	stomach
14	chr2:178471800-178482600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:178472400-178474800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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