Variant report

Variant	rs618998
Chromosome Location	chr6:11516282-11516283
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM170B-2	chr6:11514425-11516699	NONHSAT107759
2	lnc-TMEM170B-2	chr6:11515828-11516747	NONHSAT107755

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10807114	0.89[ASN][1000 genomes]
rs10807115	0.89[ASN][1000 genomes]
rs10947357	0.82[YRI][hapmap]
rs11751884	0.88[ASN][1000 genomes]
rs11755780	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11756371	0.88[ASN][1000 genomes]
rs12192094	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12198765	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12198774	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12198950	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12200391	0.89[ASN][1000 genomes]
rs12200454	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12211930	0.82[YRI][hapmap]
rs12529805	0.82[YRI][hapmap]
rs17697397	0.82[YRI][hapmap]
rs1923525	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025184	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2025185	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2758307	0.81[ASN][1000 genomes]
rs2807964	0.81[ASN][1000 genomes]
rs4711306	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4713593	0.86[ASN][1000 genomes]
rs4713594	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4713618	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs478147	0.80[CEU][hapmap]
rs480684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487729	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs490327	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs490466	0.80[CEU][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap]
rs493183	0.89[ASN][1000 genomes]
rs505839	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518183	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs528012	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs528087	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs533319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554671	0.80[CEU][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap]
rs555034	0.80[EUR][1000 genomes]
rs555742	0.80[CEU][hapmap]
rs562508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568867	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs570714	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs575164	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588062	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs588948	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594164	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs595877	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs598907	0.80[CEU][hapmap]
rs601505	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606402	0.80[CEU][hapmap]
rs609135	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs616729	0.81[ASN][1000 genomes]
rs617157	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618573	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs620867	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs623024	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs628980	0.80[CEU][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap]
rs671048	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675565	0.80[CEU][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap]
rs678862	0.80[CEU][hapmap]
rs681483	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs685384	0.80[CEU][hapmap]
rs6899820	0.85[EUR][1000 genomes]
rs6901328	0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6907796	0.89[ASN][1000 genomes]
rs6913697	0.86[ASN][1000 genomes]
rs6914208	0.83[ASN][1000 genomes]
rs6914420	0.86[ASN][1000 genomes]
rs6915153	0.86[ASN][1000 genomes]
rs6915366	0.86[ASN][1000 genomes]
rs6926422	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6941011	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6941700	0.86[ASN][1000 genomes]
rs9348892	0.86[ASN][1000 genomes]
rs9348895	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9348896	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9357154	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9366806	0.88[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9368728	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9394102	0.86[JPT][hapmap]
rs9394115	0.80[CEU][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap]
rs9394117	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9394123	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394154	0.86[CHB][hapmap];0.82[JPT][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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv600989	chr6:11509323-11581990	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs618998	GCNT2	cis	cerebellum	SCAN
rs618998	TMEM170B	cis	Adipose Subcutaneous	GTEx
rs618998	TMEM170B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11514200-11516600	Flanking Active TSS	GM12878-XiMat	blood
2	chr6:11515400-11516600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr6:11515600-11518600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr6:11515600-11518600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:11516200-11519000	Weak transcription	Primary B cells from cord blood	blood

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