Variant report

Variant	rs11742445
Chromosome Location	chr5:57285867-57285868
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:57279398..57281900-chr5:57285710..57288017,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10472030	0.95[ASN][1000 genomes]
rs11738952	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11740997	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11741208	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11741819	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11744663	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11749915	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13160441	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1349957	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1352609	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1352610	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1378248	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387641	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1454918	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1454920	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1454924	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1454925	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1454926	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1454928	0.85[AMR][1000 genomes]
rs1489791	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1489797	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17749982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1821210	1.00[ASW][hapmap]
rs1826101	0.96[AMR][1000 genomes]
rs1826106	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1844437	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2408854	1.00[ASW][hapmap]
rs4403130	1.00[ASW][hapmap]
rs4458541	1.00[ASW][hapmap]
rs4699913	1.00[ASW][hapmap]
rs4699920	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4700233	1.00[ASW][hapmap]
rs4700243	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4700244	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4700245	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56976559	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60707702	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61636750	0.89[AMR][1000 genomes]
rs62359093	0.89[AMR][1000 genomes]
rs62359098	0.89[AMR][1000 genomes]
rs62359143	0.81[ASN][1000 genomes]
rs62359144	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62359145	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62359146	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62359147	0.83[ASN][1000 genomes]
rs62359148	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62360185	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62360186	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62360187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62360200	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62368373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368399	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62368400	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368401	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368402	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368403	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62368405	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368406	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368407	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368408	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368409	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368410	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62368411	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62368412	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62368413	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62368414	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62368415	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6450458	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6884729	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6886096	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7713227	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7736576	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs984926	0.96[AMR][1000 genomes];0.85[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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1792273	chr5:57214817-57320343	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv10700	chr5:57277483-57313710	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv1817904	chr5:57277522-57359476	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1829717	chr5:57277522-57359476	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1830976	chr5:57277522-57359476	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1837615	chr5:57277522-57359476	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1846984	chr5:57277522-57359476	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1850205	chr5:57277522-57359476	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11742445	SLC38A9	cis	parietal	SCAN
rs11742445	MAP3K1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57284600-57286200	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr5:57284600-57286200	Enhancers	NHEK	skin
3	chr5:57285200-57286000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:57285200-57289200	Weak transcription	Left Ventricle	heart
5	chr5:57285200-57297600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:57285400-57286000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr5:57285800-57286200	Enhancers	A549	lung

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