Variant report

Variant	rs1799808
Chromosome Location	chr2:128175862-128175863
allele	C/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	NR3C1	chr2:128175749-128176036	A549	lung:	n/a	chr2:128175890-128175916
2	HEY1	chr2:128175747-128177435	HepG2	liver:	n/a	n/a
3	HDAC2	chr2:128175654-128176798	HepG2	liver:	n/a	n/a
4	MAFK	chr2:128175680-128176609	HepG2	liver:	n/a	chr2:128176345-128176360
5	MAX	chr2:128175811-128176712	HepG2	liver:	n/a	chr2:128176450-128176460 chr2:128176449-128176459 chr2:128176449-128176460 chr2:128176253-128176262 chr2:128176450-128176460 chr2:128176448-128176461 chr2:128176448-128176461 chr2:128176449-128176460 chr2:128176450-128176459 chr2:128176449-128176460 chr2:128176448-128176461 chr2:128176449-128176459 chr2:128176445-128176464
6	FOXA1	chr2:128175639-128177255	HepG2	liver:	n/a	n/a
7	RAD21	chr2:128175711-128176725	HepG2	liver:	n/a	chr2:128176113-128176126 chr2:128176211-128176224 chr2:128176524-128176533
8	TAF1	chr2:128175758-128176704	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:128175737-128177495	HepG2	liver:	n/a	n/a
10	NR3C1	chr2:128175761-128176032	A549	lung:	n/a	chr2:128175890-128175916
11	TBP	chr2:128175790-128177251	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:128175695-128176789	HepG2	liver:	n/a	n/a
13	NR3C1	chr2:128175707-128176158	A549	lung:	n/a	chr2:128175890-128175916
14	MAFF	chr2:128175790-128176217	HepG2	liver:	n/a	n/a
15	CHD2	chr2:128175791-128176524	HepG2	liver:	n/a	n/a
16	MYBL2	chr2:128175595-128177696	HepG2	liver:	n/a	n/a
17	CEBPD	chr2:128175744-128176733	HepG2	liver:	n/a	n/a
18	NFIC	chr2:128175695-128176874	HepG2	liver:	n/a	n/a
19	MBD4	chr2:128175663-128177420	HepG2	liver:	n/a	n/a
20	CEBPB	chr2:128175845-128176121	HepG2	liver:	n/a	n/a
21	MAZ	chr2:128175772-128176499	HepG2	liver:	n/a	chr2:128176450-128176460 chr2:128176449-128176459 chr2:128176449-128176460 chr2:128176253-128176262 chr2:128176450-128176460 chr2:128176448-128176461 chr2:128176448-128176461 chr2:128176449-128176460 chr2:128176450-128176459 chr2:128176449-128176460 chr2:128176448-128176461 chr2:128176449-128176459 chr2:128176445-128176464
22	MAX	chr2:128175611-128177655	HepG2	liver:	n/a	chr2:128176450-128176460 chr2:128176449-128176459 chr2:128176449-128176460 chr2:128176253-128176262 chr2:128176450-128176460 chr2:128176448-128176461 chr2:128176448-128176461 chr2:128176449-128176460 chr2:128176450-128176459 chr2:128176449-128176460 chr2:128176448-128176461 chr2:128176449-128176459 chr2:128176445-128176464
23	SP1	chr2:128175662-128176731	HepG2	liver:	n/a	n/a
24	TEAD4	chr2:128175515-128177422	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:128175249-128180723	HepG2	liver:	n/a	n/a
26	MXI1	chr2:128175753-128176714	HepG2	liver:	n/a	chr2:128176451-128176460 chr2:128176449-128176458 chr2:128176451-128176460 chr2:128176449-128176458
27	POLR2A	chr2:128175695-128177493	HepG2	liver:	n/a	n/a
28	NFIC	chr2:128175606-128177482	HepG2	liver:	n/a	n/a
29	YY1	chr2:128175737-128176947	HepG2	liver:	n/a	chr2:128176612-128176628 chr2:128176616-128176625
30	MBD4	chr2:128175614-128177601	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:128175672-128177814	HepG2	liver:	n/a	n/a
32	NR3C1	chr2:128175703-128176182	A549	lung:	n/a	chr2:128175890-128175916
33	FOXA2	chr2:128175724-128176997	HepG2	liver:	n/a	n/a
34	MYC	chr2:128175784-128176829	HepG2	liver:	n/a	chr2:128176450-128176460 chr2:128176449-128176459 chr2:128176449-128176460 chr2:128176253-128176262 chr2:128176450-128176460 chr2:128176448-128176461 chr2:128176448-128176461 chr2:128176449-128176460 chr2:128176450-128176459 chr2:128176449-128176460 chr2:128176448-128176461 chr2:128176449-128176459 chr2:128176445-128176464
35	TAF1	chr2:128175751-128176818	HepG2	liver:	n/a	n/a
36	YY1	chr2:128175741-128176783	HepG2	liver:	n/a	chr2:128176612-128176628 chr2:128176616-128176625
37	RFX5	chr2:128175768-128176256	HepG2	liver:	n/a	n/a
38	ZBTB7A	chr2:128175792-128176611	HepG2	liver:	n/a	n/a
39	RCOR1	chr2:128175765-128176986	HepG2	liver:	n/a	n/a
40	EP300	chr2:128175800-128176773	HepG2	liver:	n/a	n/a
41	FOXA1	chr2:128175639-128176306	HepG2	liver:	n/a	n/a
42	BHLHE40	chr2:128175803-128176744	HepG2	liver:	n/a	n/a
43	REST	chr2:128175731-128176465	HepG2	liver:	n/a	n/a
44	HEY1	chr2:128175687-128177560	HepG2	liver:	n/a	n/a
45	ZBTB7A	chr2:128175768-128176703	HepG2	liver:	n/a	n/a
46	POLR2A	chr2:128175857-128176609	HepG2	liver:	n/a	n/a
47	HNF4G	chr2:128175757-128176725	HepG2	liver:	n/a	chr2:128176274-128176286 chr2:128176273-128176286 chr2:128176271-128176286 chr2:128176274-128176286 chr2:128176190-128176204 chr2:128176273-128176286
48	MYBL2	chr2:128175540-128177606	HepG2	liver:	n/a	n/a
49	SMC3	chr2:128175808-128176956	HepG2	liver:	n/a	chr2:128176525-128176533 chr2:128176491-128176498
50	NR3C1	chr2:128175708-128176103	A549	lung:	n/a	chr2:128175890-128175916

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128050076..128053017-chr2:128173952..128176764,3	MCF-7	breast:

Variant related genes	Relation type
PROC	TF binding region
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10803585	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11901355	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12052483	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12463538	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12468304	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12476767	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12478656	0.84[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12622436	0.93[ASW][hapmap];0.81[MEX][hapmap]
rs12991768	0.85[EUR][1000 genomes]
rs13029237	0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1401296	0.86[ASN][1000 genomes]
rs1518759	0.87[ASN][1000 genomes]
rs1566823	0.80[ASW][hapmap]
rs1967425	0.85[ASN][1000 genomes]
rs2069912	0.98[ASN][1000 genomes]
rs2069914	0.97[ASN][1000 genomes]
rs2069915	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2069916	0.91[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2069920	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2069921	0.94[ASN][1000 genomes]
rs2069924	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2069931	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2069933	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2090574	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4150477	0.93[ASW][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap]
rs4150496	0.93[ASW][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap]
rs4233583	0.85[YRI][hapmap]
rs4497825	0.82[MEX][hapmap]
rs4662580	0.80[ASW][hapmap]
rs4662725	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4662729	0.84[ASN][1000 genomes]
rs4662730	0.91[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs5936	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs62160261	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62160290	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6710535	0.80[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6728362	0.86[ASN][1000 genomes]
rs6731176	0.82[MEX][hapmap]
rs6749002	0.83[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs6754772	0.83[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs6754999	0.80[ASW][hapmap];0.83[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7580658	0.93[ASW][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7587639	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9636237	0.80[ASW][hapmap]
rs971207	0.94[ASN][1000 genomes]
rs973760	0.94[ASN][1000 genomes]
rs9789510	0.80[AMR][1000 genomes];0.85[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	nsv583036	chr2:128173819-128183914	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1799808	ERCC3	cis	parietal	SCAN
rs1799808	ERCC3	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128172800-128176800	Weak transcription	NHDF-Ad	bronchial
2	chr2:128174000-128177800	Enhancers	A549	lung
3	chr2:128174000-128180600	Weak transcription	Right Atrium	heart
4	chr2:128174400-128176800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:128174800-128180400	Weak transcription	Spleen	Spleen
6	chr2:128175000-128177200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:128175000-128180000	Weak transcription	Primary B cells from cord blood	blood
8	chr2:128175200-128176000	Flanking Active TSS	HepG2	liver
9	chr2:128175200-128176200	Enhancers	Dnd41	blood
10	chr2:128175600-128177800	Weak transcription	Fetal Thymus	thymus
11	chr2:128175800-128176200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:128175800-128176400	Enhancers	Pancreas	Pancrea
13	chr2:128175800-128176800	Enhancers	Gastric	stomach
14	chr2:128175800-128177200	Flanking Active TSS	Liver	Liver

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