Variant report

Variant	rs4024
Chromosome Location	chr4:74301384-74301385
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	NFIC	chr4:74301325-74304839	HepG2	liver:	n/a	chr4:74301812-74301828 chr4:74301812-74301829
2	POLR2A	chr4:74301174-74301776	K562	blood:	n/a	n/a

Variant related genes	Relation type
AFP	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10002756	0.96[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs10002903	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10020432	0.96[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs10022167	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10022463	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10031441	0.83[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12503222	0.84[AMR][1000 genomes]
rs12504308	0.94[EUR][1000 genomes]
rs12506899	0.96[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12510644	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12649712	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13104065	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13114289	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13122972	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13125875	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13135376	0.80[AMR][1000 genomes]
rs13138260	0.82[AMR][1000 genomes]
rs13138734	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1475934	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs16849341	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16849384	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051510	0.82[AMR][1000 genomes]
rs2051512	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs2070849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236766	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2236767	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2276937	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298839	0.83[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs28532518	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28585480	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35545060	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3756066	0.94[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs3775485	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3775486	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes]
rs3796676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796677	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796678	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4076	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4270557	0.84[AMR][1000 genomes]
rs4345146	0.82[AMR][1000 genomes]
rs4403016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4429703	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4513532	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs4530599	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4560374	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4575963	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4621399	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4694164	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4694600	0.83[EUR][1000 genomes]
rs4694608	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4694609	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4694613	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58395249	0.84[AMR][1000 genomes]
rs6446931	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6810745	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6818116	0.84[AMR][1000 genomes]
rs6820167	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap]
rs6832260	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6832557	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6850155	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6853164	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap]
rs714825	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs7434765	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7660680	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7668327	0.89[EUR][1000 genomes]
rs7682895	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7683385	0.80[AMR][1000 genomes]
rs7688274	0.94[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs962004	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs962005	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9784408	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9784582	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9996318	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9999209	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][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	esv3430875	chr4:74243646-74420354	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4024	CCNG2	cis	cerebellum	SCAN
rs4024	ALB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74298600-74310800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:74299200-74301400	Weak transcription	Fetal Intestine Large	intestine
3	chr4:74299800-74301400	Weak transcription	Fetal Intestine Small	intestine
4	chr4:74300400-74307600	Weak transcription	Liver	Liver
5	chr4:74301200-74301800	Flanking Active TSS	HepG2	liver

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