Variant report

Variant	rs10874426
Chromosome Location	chr1:84451820-84451821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr1:84451482-84451983	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84451281..84453143-chr1:84459499..84461189,2	K562	blood:

Variant related genes	Relation type
TTLL7-IT1	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10127737	1.00[CEU][hapmap];0.91[YRI][hapmap];0.96[EUR][1000 genomes]
rs10493741	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10493744	0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs10874423	0.91[EUR][1000 genomes]
rs10874424	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11163862	0.85[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs11163865	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs11163866	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs11163867	0.89[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11163872	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11163874	0.82[AMR][1000 genomes]
rs11163875	0.82[AMR][1000 genomes]
rs11163876	0.83[AMR][1000 genomes]
rs11163877	0.84[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11163878	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs11163879	0.83[AMR][1000 genomes]
rs11807807	0.82[AMR][1000 genomes]
rs12070578	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.88[EUR][1000 genomes]
rs12118434	0.83[MEX][hapmap]
rs12139191	0.85[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12141272	0.85[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12145258	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12146038	0.81[AMR][1000 genomes]
rs12730621	0.85[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12749350	0.85[CEU][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12757632	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs12759527	0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs1324486	0.85[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1359331	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[EUR][1000 genomes]
rs1570691	0.85[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1871924	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1871925	0.84[AMR][1000 genomes]
rs1952065	0.85[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1952066	0.85[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2024591	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs2147392	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2389617	0.85[CEU][hapmap]
rs2389648	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2389649	0.91[EUR][1000 genomes]
rs28445286	0.82[AMR][1000 genomes]
rs28567085	0.82[AMR][1000 genomes]
rs34155960	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35946036	0.83[AMR][1000 genomes]
rs35969331	0.84[AMR][1000 genomes]
rs4258241	0.84[MEX][hapmap]
rs4907185	0.82[EUR][1000 genomes]
rs4907186	1.00[CEU][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs4907188	0.96[EUR][1000 genomes]
rs4907190	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4907191	0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs6663949	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670658	0.85[AMR][1000 genomes]
rs6687372	0.84[AMR][1000 genomes]
rs6694752	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6699501	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6703382	0.82[AMR][1000 genomes]
rs6703493	0.84[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7550413	0.81[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7551787	0.82[ASW][hapmap];0.85[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs882897	0.85[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs942848	0.82[AMR][1000 genomes]
rs942849	0.82[AMR][1000 genomes]
rs980417	0.96[CEU][hapmap];0.96[YRI][hapmap];0.96[EUR][1000 genomes]
rs980418	0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871551	chr1:84354464-84453223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10874426	NKX1-2	trans	parietal	SCAN
rs10874426	LPHN2	cis	parietal	SCAN
rs10874426	DNASE2B	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84425200-84453200	Weak transcription	NHLF	lung
2	chr1:84426200-84452200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:84436600-84452200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:84446200-84461800	Weak transcription	Aorta	Aorta
5	chr1:84451200-84461000	Weak transcription	Gastric	stomach
6	chr1:84451200-84464000	Weak transcription	Pancreas	Pancrea
7	chr1:84451400-84462200	Weak transcription	Stomach Mucosa	stomach

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