Variant report

Variant	rs1517744
Chromosome Location	chr1:169423810-169423811
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: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10429893	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10465575	0.81[ASN][1000 genomes]
rs10465576	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10489189	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10732287	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10737546	0.80[EUR][1000 genomes]
rs10800424	0.82[JPT][hapmap]
rs10800425	0.82[JPT][hapmap]
rs10800435	0.82[JPT][hapmap]
rs10800438	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10800440	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10800447	0.92[CEU][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs10919124	0.82[JPT][hapmap]
rs10919168	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919173	0.92[CEU][hapmap]
rs10919174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1124843	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1133814	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12029566	0.81[ASN][1000 genomes]
rs12076993	0.82[AMR][1000 genomes]
rs1208134	1.00[ASN][1000 genomes]
rs1208135	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1208327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1400836	0.87[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1517745	0.96[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1517747	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]
rs1591733	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs1856303	0.82[JPT][hapmap]
rs1914505	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1983546	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2003653	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2037250	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs2138898	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2176473	0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs3766095	0.82[JPT][hapmap]
rs3820059	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3905328	0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.81[ASN][1000 genomes]
rs4264046	0.82[JPT][hapmap]
rs4656183	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4656672	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6427185	0.87[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap]
rs6427187	0.81[ASN][1000 genomes]
rs6656822	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6669901	0.81[ASN][1000 genomes]
rs6672589	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6700375	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415756	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7521582	0.87[CHD][hapmap]
rs7524348	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs7533257	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs7544221	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs760603	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs925892	0.81[ASN][1000 genomes]
rs9287089	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs932301	0.82[AMR][1000 genomes];0.81[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1517744	NME7	cis	Thyroid	GTEx
rs1517744	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs1517744	KIFAP3	cis	cerebellum	SCAN

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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