Variant report

Variant	rs12062871
Chromosome Location	chr1:224653597-224653598
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224645408..224648550-chr1:224650858..224654034,4	K562	blood:
2	chr1:224620532..224622237-chr1:224651985..224654670,2	K562	blood:
3	chr1:224644724..224648422-chr1:224649777..224653927,3	K562	blood:

Variant related genes	Relation type
ENSG00000162923	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10127813	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10127953	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10128058	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10159333	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495219	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10753465	0.85[EUR][1000 genomes]
rs10753466	0.85[EUR][1000 genomes]
rs10753467	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10753468	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10799569	0.85[EUR][1000 genomes]
rs10916606	0.84[EUR][1000 genomes]
rs10916607	0.84[EUR][1000 genomes]
rs10916614	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10916616	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916617	0.98[EUR][1000 genomes]
rs10916619	0.98[EUR][1000 genomes]
rs11576835	0.84[EUR][1000 genomes]
rs11577170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11577183	0.84[EUR][1000 genomes]
rs11578709	0.92[EUR][1000 genomes]
rs11579952	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11584057	0.89[EUR][1000 genomes]
rs11584247	0.84[EUR][1000 genomes]
rs11584638	0.95[EUR][1000 genomes]
rs11584980	0.84[EUR][1000 genomes]
rs11586729	0.84[EUR][1000 genomes]
rs11588973	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11590658	0.98[EUR][1000 genomes]
rs11800613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11801436	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11801645	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11803414	0.86[EUR][1000 genomes]
rs11803981	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11805973	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11807763	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11807942	0.84[EUR][1000 genomes]
rs11811053	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12731035	0.87[EUR][1000 genomes]
rs12731630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12738799	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12739486	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12740255	0.84[EUR][1000 genomes]
rs12742821	0.84[EUR][1000 genomes]
rs12742989	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12743200	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12745610	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12747286	0.92[EUR][1000 genomes]
rs12751161	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12754832	0.84[EUR][1000 genomes]
rs12755338	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12755816	0.85[EUR][1000 genomes]
rs12758302	0.90[EUR][1000 genomes]
rs12758579	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12759275	0.84[EUR][1000 genomes]
rs1539207	0.85[EUR][1000 genomes]
rs1544196	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16848365	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17503938	0.84[EUR][1000 genomes]
rs17570292	0.90[EUR][1000 genomes]
rs2185684	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28434172	0.92[EUR][1000 genomes]
rs2897048	0.93[EUR][1000 genomes]
rs34791963	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35011635	0.94[EUR][1000 genomes]
rs35031726	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35067427	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35169600	0.83[EUR][1000 genomes]
rs35277713	0.95[EUR][1000 genomes]
rs35303987	0.95[EUR][1000 genomes]
rs35341841	0.81[EUR][1000 genomes]
rs35365551	0.91[EUR][1000 genomes]
rs35571080	0.98[EUR][1000 genomes]
rs35767322	0.90[EUR][1000 genomes]
rs35804313	0.92[EUR][1000 genomes]
rs35915186	0.96[EUR][1000 genomes]
rs35972228	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36138926	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4653587	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4654037	0.85[EUR][1000 genomes]
rs55730749	0.98[EUR][1000 genomes]
rs56223447	0.84[EUR][1000 genomes]
rs6426121	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6426123	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6426125	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6426126	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66467176	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66530931	0.82[EUR][1000 genomes]
rs6663522	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6671751	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6672859	0.85[EUR][1000 genomes]
rs6675858	0.84[EUR][1000 genomes]
rs6691779	0.84[EUR][1000 genomes]
rs6693287	0.84[EUR][1000 genomes]
rs6698343	0.90[EUR][1000 genomes]
rs6701145	0.84[EUR][1000 genomes]
rs67065875	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68037178	0.83[EUR][1000 genomes]
rs71644786	0.91[EUR][1000 genomes]
rs7365151	0.98[EUR][1000 genomes]
rs7512431	0.85[EUR][1000 genomes]
rs7513208	0.84[EUR][1000 genomes]
rs7514284	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7514575	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7517754	0.85[EUR][1000 genomes]
rs7518109	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7519734	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7522956	0.85[EUR][1000 genomes]
rs7527044	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7529067	0.85[EUR][1000 genomes]
rs7529310	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs867362	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs885606	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9970697	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12062871	CNIH4	cis	Heart Left Ventricle	GTEx
rs12062871	CNIH4	cis	Thyroid	GTEx
rs12062871	CNIH4	cis	Esophagus Muscularis	GTEx
rs12062871	CNIH4	cis	Muscle Skeletal	GTEx
rs12062871	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs12062871	CNIH4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224628600-224653600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:224645400-224656200	Weak transcription	Primary T cells from cord blood	blood
3	chr1:224653000-224654200	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr1:224653200-224654000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:224653200-224654000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:224653200-224654000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:224653200-224654200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr1:224653200-224654200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:224653400-224653600	Enhancers	GM12878-XiMat	blood
10	chr1:224653400-224653800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr1:224653400-224653800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:224653400-224654000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr1:224653400-224654200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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