Variant report

Variant	rs1018828
Chromosome Location	chr1:169557734-169557735
allele	G/T
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	JUN	chr1:169557298-169557833	HepG2	liver:	n/a	n/a
2	TEAD4	chr1:169557174-169557850	HepG2	liver:	n/a	n/a
3	HNF4A	chr1:169557315-169557818	HepG2	liver:	n/a	chr1:169557693-169557701 chr1:169557515-169557530 chr1:169557515-169557530 chr1:169557516-169557528
4	MYBL2	chr1:169557115-169557758	HepG2	liver:	n/a	n/a
5	HDAC2	chr1:169557251-169557758	HepG2	liver:	n/a	chr1:169557694-169557703
6	TCF7L2	chr1:169557542-169557734	HepG2	liver:	n/a	n/a
7	EP300	chr1:169557256-169557741	HepG2	liver:	n/a	chr1:169557317-169557325 chr1:169557694-169557704
8	HNF4G	chr1:169557330-169557742	HepG2	liver:	n/a	chr1:169557693-169557701 chr1:169557515-169557530 chr1:169557513-169557528 chr1:169557515-169557530 chr1:169557516-169557528
9	CEBPB	chr1:169557445-169557832	HepG2	liver:	n/a	chr1:169557645-169557656
10	ARID3A	chr1:169557339-169558326	HepG2	liver:	n/a	n/a
11	EP300	chr1:169557385-169557743	HepG2	liver:	n/a	chr1:169557694-169557704
12	FOXA2	chr1:169557357-169557828	HepG2	liver:	n/a	n/a
13	MAFK	chr1:169557468-169558042	HepG2	liver:	n/a	chr1:169557956-169557970 chr1:169557958-169557969 chr1:169557957-169557973 chr1:169557957-169557968 chr1:169557957-169557968
14	CEBPB	chr1:169557411-169557791	HepG2	liver:	n/a	chr1:169557645-169557656
15	JUND	chr1:169557400-169557806	HepG2	liver:	n/a	n/a
16	NFIC	chr1:169557356-169557795	HepG2	liver:	n/a	n/a
17	FOXA1	chr1:169557433-169557799	HepG2	liver:	n/a	n/a
18	SMC3	chr1:169557526-169557772	HepG2	liver:	n/a	n/a
19	HNF4G	chr1:169557159-169557764	HepG2	liver:	n/a	chr1:169557693-169557701 chr1:169557515-169557530 chr1:169557254-169557262 chr1:169557513-169557528 chr1:169557515-169557530 chr1:169557253-169557268 chr1:169557516-169557528
20	HNF4A	chr1:169557424-169557767	HepG2	liver:	n/a	chr1:169557693-169557701 chr1:169557515-169557530 chr1:169557515-169557530 chr1:169557516-169557528
21	SP1	chr1:169557329-169557741	HepG2	liver:	n/a	n/a
22	HDAC2	chr1:169557362-169557842	HepG2	liver:	n/a	chr1:169557694-169557703
23	NFIC	chr1:169557345-169557870	HepG2	liver:	n/a	n/a
24	EP300	chr1:169557357-169557792	HepG2	liver:	n/a	chr1:169557694-169557704
25	FOXA1	chr1:169557319-169557993	HepG2	liver:	n/a	n/a
26	MYBL2	chr1:169557160-169557761	HepG2	liver:	n/a	n/a
27	FOXA1	chr1:169557249-169557953	HepG2	liver:	n/a	n/a
28	FOXA1	chr1:169557374-169557804	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169555910..169558714-chr1:169805893..169807663,2	K562	blood:

Variant related genes	Relation type
F5	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10489184	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569471	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16862374	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862375	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862377	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862380	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17522707	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs17587779	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3917787	0.81[EUR][1000 genomes]
rs3917788	0.81[EUR][1000 genomes]
rs3917793	0.81[EUR][1000 genomes]
rs3917794	0.81[EUR][1000 genomes]
rs3917810	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3917818	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs3917827	0.84[EUR][1000 genomes]
rs3917832	0.91[ASW][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs3917836	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3917839	0.98[EUR][1000 genomes]
rs3917840	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3917848	1.00[JPT][hapmap];0.93[YRI][hapmap]
rs3917851	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3917853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs3917855	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs3917873	0.81[EUR][1000 genomes]
rs57207056	0.92[AFR][1000 genomes]
rs6023	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61280985	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6664922	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703487	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703865	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73037471	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7528914	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332476	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332479	0.81[AFR][1000 genomes]
rs9332480	0.83[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9332482	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9332486	0.92[AFR][1000 genomes]
rs9332489	0.92[AFR][1000 genomes]
rs9332491	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9332492	0.91[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9332494	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9332496	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9332504	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332517	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332562	0.92[EUR][1000 genomes];1.00[ASN][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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv548187	chr1:169530837-169559035	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv872534	chr1:169533266-169561274	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1018828	POGK	cis	parietal	SCAN
rs1018828	SELP	cis	parietal	SCAN
rs1018828	METTL13	cis	parietal	SCAN
rs1018828	FMO6P	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169555800-169558800	Enhancers	Primary T cells from cord blood	blood
2	chr1:169556200-169558200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:169556200-169558800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:169556200-169559200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:169556400-169557800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:169556400-169557800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:169556400-169558000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:169556400-169558000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr1:169556400-169558000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:169556400-169558000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:169556400-169558000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:169556400-169558000	Weak transcription	Dnd41	blood
13	chr1:169556400-169558200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:169556400-169558600	Enhancers	Liver	Liver
15	chr1:169556400-169558800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:169556400-169562000	Weak transcription	GM12878-XiMat	blood
17	chr1:169556600-169558000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:169556600-169558600	Enhancers	HepG2	liver
19	chr1:169557400-169557800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:169557400-169558800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:169557400-169558800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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