Variant report

Variant	rs12731630
Chromosome Location	chr1:224650947-224650948
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	chr1:224645408..224648550-chr1:224650858..224654034,4	K562	blood:
2	chr1:224644724..224648422-chr1:224649777..224653927,3	K562	blood:

Extended variants
information (count: 119 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10127813	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10127953	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10128058	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10159333	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10495219	1.00[CEU][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10753465	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10753466	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10753467	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10753468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799569	0.86[EUR][1000 genomes]
rs10799573	0.82[MEX][hapmap]
rs10799574	0.82[MEX][hapmap]
rs10916606	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10916607	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10916614	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916616	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10916617	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10916619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11576835	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11577170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577183	0.86[EUR][1000 genomes]
rs11578709	0.90[EUR][1000 genomes]
rs11579952	0.95[CEU][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11584057	0.88[EUR][1000 genomes]
rs11584247	0.85[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11584980	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11586729	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11588973	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs11800613	1.00[CEU][hapmap];1.00[CHB][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]
rs11801436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11801645	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11803414	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs11803981	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11805973	0.95[CEU][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11807763	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11807942	0.86[EUR][1000 genomes]
rs11811053	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12062871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12731035	0.88[EUR][1000 genomes]
rs12738799	1.00[CEU][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12739486	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12740255	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12742821	0.86[EUR][1000 genomes]
rs12742989	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12743200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745610	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12747286	0.94[EUR][1000 genomes]
rs12751161	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12754832	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12755338	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs12758302	0.92[EUR][1000 genomes]
rs12758579	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12759275	0.86[EUR][1000 genomes]
rs1539207	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1544196	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16848365	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17503938	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17570292	0.89[EUR][1000 genomes]
rs2185684	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28434172	0.94[EUR][1000 genomes]
rs2897048	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs34791963	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35011635	0.96[EUR][1000 genomes]
rs35031726	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35067427	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35169600	0.84[EUR][1000 genomes]
rs35277713	0.96[EUR][1000 genomes]
rs35303987	0.96[EUR][1000 genomes]
rs35341841	0.83[EUR][1000 genomes]
rs35365551	0.92[EUR][1000 genomes]
rs35571080	0.99[EUR][1000 genomes]
rs35767322	0.92[EUR][1000 genomes]
rs35804313	0.90[EUR][1000 genomes]
rs35915186	0.95[EUR][1000 genomes]
rs35972228	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36138926	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4653585	1.00[CEU][hapmap]
rs4653587	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4654037	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs55730749	0.99[EUR][1000 genomes]
rs56223447	0.86[EUR][1000 genomes]
rs6426121	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6426123	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6426125	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6426126	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66467176	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66530931	0.80[EUR][1000 genomes]
rs6663522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671751	0.95[CEU][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6672859	0.86[EUR][1000 genomes]
rs6675858	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6691779	0.95[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs6693287	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs6698343	0.89[EUR][1000 genomes]
rs6701145	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs67065875	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs68037178	0.84[EUR][1000 genomes]
rs71644786	0.92[EUR][1000 genomes]
rs7365151	0.99[EUR][1000 genomes]
rs7512431	0.86[EUR][1000 genomes]
rs7513208	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7514284	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[GIH][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7514575	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7517754	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7518109	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7519734	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7522956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs7527044	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7529067	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7529310	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs867362	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs885606	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9970697	0.86[AMR][1000 genomes];0.99[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12731630	CNIH4	cis	Heart Left Ventricle	GTEx
rs12731630	CNIH4	cis	multi-tissue	Pritchard
rs12731630	CNIH4	cis	Muscle Skeletal	GTEx
rs12731630	CNIH4	cis	parietal	SCAN
rs12731630	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs12731630	CNIH4	cis	Adipose Subcutaneous	GTEx
rs12731630	CNIH4	cis	Esophagus Mucosa	GTEx
rs12731630	CNIH4	cis	Esophagus Muscularis	GTEx
rs12731630	CNIH4	cis	Thyroid	GTEx

Chromatin state (count:8 , 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	chr1:224644800-224651200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:224645400-224652000	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:224645400-224653400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:224645400-224653400	Weak transcription	GM12878-XiMat	blood
6	chr1:224645400-224656200	Weak transcription	Primary T cells from cord blood	blood
7	chr1:224647600-224651400	Weak transcription	Fetal Brain Male	brain
8	chr1:224648400-224652800	Weak transcription	K562	blood

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