Variant report

Variant	rs1517745
Chromosome Location	chr1:169423795-169423796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169417406..169419368-chr1:169421351..169424110,2	K562	blood:
2	chr1:169335871..169338700-chr1:169422352..169424745,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC19A2-1	chr1:169423738-169423818	ENSG00000234437.1
2	lnc-SLC19A2-1	chr1:169423629-169423818	ENSG00000234437.1

Variant related genes	Relation type
ENSG00000143156	Chromatin interaction
ENSG00000117475	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10158131	0.88[CHB][hapmap];0.80[CHD][hapmap]
rs1028180	0.89[CHB][hapmap]
rs10737546	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10753786	0.94[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap]
rs10800447	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10919132	0.88[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs10919140	0.88[CHB][hapmap]
rs10919173	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919174	0.96[CEU][hapmap]
rs12121994	0.89[CHB][hapmap]
rs12143193	0.89[CHB][hapmap]
rs12145146	0.83[CHB][hapmap]
rs12145226	0.89[CHB][hapmap]
rs12733001	0.88[CHB][hapmap]
rs12733037	0.82[CHB][hapmap]
rs12733626	0.88[CHB][hapmap]
rs12752953	0.88[CHB][hapmap]
rs1517743	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1517744	0.96[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1517747	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1533518	0.89[CHB][hapmap]
rs16862081	0.89[CHB][hapmap]
rs16862097	0.87[CHB][hapmap]
rs16862176	0.89[CHB][hapmap]
rs16862180	0.89[CHB][hapmap]
rs16862217	0.81[CHB][hapmap]
rs1883167	0.89[CHB][hapmap]
rs2037249	0.89[CHB][hapmap]
rs2066001	0.89[CHB][hapmap]
rs2271762	0.89[CHB][hapmap]
rs2300157	0.88[CHB][hapmap]
rs2300158	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2420015	0.89[CHB][hapmap]
rs2420016	0.89[CHB][hapmap]
rs3213586	0.89[CHB][hapmap]
rs3213587	0.88[CHB][hapmap]
rs3766090	0.88[CHB][hapmap]
rs3862937	0.88[CHB][hapmap]
rs4140538	0.88[CHB][hapmap]
rs4140539	0.87[CHB][hapmap]
rs6656822	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs6672589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6697727	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524348	0.96[CEU][hapmap]
rs929133	0.82[CHB][hapmap]

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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1517745	NME7	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169418600-169429200	Weak transcription	Stomach Mucosa	stomach

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