Variant report

Variant	rs289904
Chromosome Location	chr2:152085643-152085644
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	chr2:152084091..152085689-chr2:152094268..152097132,2	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10165186	0.85[EUR][1000 genomes]
rs10165284	0.85[EUR][1000 genomes]
rs10184314	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10201139	0.85[EUR][1000 genomes]
rs10203366	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10207408	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10209942	0.85[EUR][1000 genomes]
rs10210155	0.85[EUR][1000 genomes]
rs10490523	0.87[ASN][1000 genomes]
rs11680338	0.90[EUR][1000 genomes]
rs11691055	0.90[EUR][1000 genomes]
rs11691217	0.90[EUR][1000 genomes]
rs12052565	0.82[ASN][1000 genomes]
rs12465426	0.87[ASN][1000 genomes]
rs12467046	0.90[EUR][1000 genomes]
rs12471191	0.90[EUR][1000 genomes]
rs12624156	0.84[EUR][1000 genomes]
rs12693004	0.84[EUR][1000 genomes]
rs12996459	0.86[EUR][1000 genomes]
rs12998170	0.86[EUR][1000 genomes]
rs13007728	0.83[EUR][1000 genomes]
rs13020769	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13020962	0.83[EUR][1000 genomes]
rs13025888	0.88[EUR][1000 genomes]
rs13027425	0.83[EUR][1000 genomes]
rs13030194	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13412131	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13420739	0.86[EUR][1000 genomes]
rs2194492	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2218880	0.88[EUR][1000 genomes]
rs2271811	0.92[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs2278089	0.86[CHB][hapmap]
rs2278090	0.84[EUR][1000 genomes]
rs28416443	0.83[EUR][1000 genomes]
rs2880489	0.81[ASN][1000 genomes]
rs289871	0.86[ASN][1000 genomes]
rs289905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289906	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs289907	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289919	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs289921	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289922	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs289923	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs289924	0.81[EUR][1000 genomes]
rs34028108	0.83[EUR][1000 genomes]
rs34092307	0.86[EUR][1000 genomes]
rs34132424	1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs34385951	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34433746	0.82[EUR][1000 genomes]
rs34538548	0.84[EUR][1000 genomes]
rs34548459	0.82[EUR][1000 genomes]
rs34639984	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35058039	0.82[ASN][1000 genomes]
rs35371567	0.86[EUR][1000 genomes]
rs35613168	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35680784	0.84[EUR][1000 genomes]
rs35791982	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs387297	0.86[CHB][hapmap]
rs403411	0.81[ASN][1000 genomes]
rs4664318	0.85[EUR][1000 genomes]
rs4664319	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4664320	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4665114	0.88[EUR][1000 genomes]
rs4665163	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4665167	0.84[EUR][1000 genomes]
rs4665168	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs4665169	0.81[EUR][1000 genomes]
rs4665170	0.84[EUR][1000 genomes]
rs55775354	0.86[EUR][1000 genomes]
rs56335263	0.84[EUR][1000 genomes]
rs56376752	0.86[EUR][1000 genomes]
rs59247111	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60956116	0.83[EUR][1000 genomes]
rs6433325	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6433327	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66521733	0.86[EUR][1000 genomes]
rs66588921	0.88[EUR][1000 genomes]
rs6705180	0.86[EUR][1000 genomes]
rs6708382	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6713041	0.81[EUR][1000 genomes]
rs6713190	0.84[EUR][1000 genomes]
rs67181317	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6723298	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6726634	0.89[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs67303849	0.87[EUR][1000 genomes]
rs6739517	0.88[EUR][1000 genomes]
rs6752471	0.83[EUR][1000 genomes]
rs6752617	0.84[EUR][1000 genomes]
rs67693192	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67725431	0.84[EUR][1000 genomes]
rs67868855	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7559296	0.88[EUR][1000 genomes]
rs7587037	0.83[EUR][1000 genomes]
rs9287955	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9287956	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9636292	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523849	chr2:151718133-152143524	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1014936	chr2:152019809-152118479	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs289904	NMI	Cis_1M	lymphoblastoid	RTeQTL
rs289904	TNFAIP6	cis	parietal	SCAN
rs289904	TNFAIP6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152085000-152086000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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