Variant report

Variant	rs2854719
Chromosome Location	chr2:208995109-208995110
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	STAT3	chr2:208994768-208995160	MCF10A-Er-Src	breast:	n/a	chr2:208994855-208994866 chr2:208994857-208994865
2	HNF4A	chr2:208994936-208995463	HepG2	liver:	n/a	chr2:208994998-208995006 chr2:208995264-208995279
3	POLR2A	chr2:208994960-208995358	HepG2	liver:	n/a	n/a
4	REST	chr2:208995048-208995451	HepG2	liver:	n/a	chr2:208995112-208995132 chr2:208995112-208995132
5	GATA3	chr2:208994494-208995408	SK-N-SH	brain:	n/a	chr2:208995025-208995032 chr2:208995025-208995032 chr2:208995021-208995037 chr2:208995018-208995039 chr2:208995024-208995032 chr2:208995025-208995032
6	EP300	chr2:208994709-208995183	SK-N-SH_RA	brain:	n/a	n/a
7	HEY1	chr2:208994999-208995366	HepG2	liver:	n/a	n/a
8	HNF4A	chr2:208994994-208995440	HepG2	liver:	n/a	chr2:208994998-208995006 chr2:208995264-208995279
9	SP1	chr2:208994792-208995517	HepG2	liver:	n/a	n/a
10	JUND	chr2:208994740-208995168	Hela-S3	cervix:	n/a	chr2:208994932-208994942 chr2:208994932-208994942 chr2:208994931-208994942 chr2:208994933-208994941
11	TEAD4	chr2:208994385-208995580	HepG2	liver:	n/a	n/a
12	GATA3	chr2:208994703-208995339	MCF-7	breast:	n/a	chr2:208995025-208995032 chr2:208995025-208995032 chr2:208995021-208995037 chr2:208995018-208995039 chr2:208995024-208995032 chr2:208995025-208995032
13	JUND	chr2:208994631-208995252	SK-N-SH	brain:	n/a	chr2:208994932-208994942 chr2:208994932-208994942 chr2:208994931-208994942 chr2:208994933-208994941
14	JUND	chr2:208994667-208995276	SK-N-SH	brain:	n/a	chr2:208994932-208994942 chr2:208994932-208994942 chr2:208994931-208994942 chr2:208994933-208994941
15	ARID3A	chr2:208994943-208995512	HepG2	liver:	n/a	n/a
16	GATA3	chr2:208994694-208995409	MCF-7	breast:	n/a	chr2:208995025-208995032 chr2:208995025-208995032 chr2:208995021-208995037 chr2:208995018-208995039 chr2:208995024-208995032 chr2:208995025-208995032
17	MYBL2	chr2:208994782-208995720	HepG2	liver:	n/a	n/a
18	RXRA	chr2:208994468-208995175	SK-N-SH	brain:	n/a	n/a
19	KAP1	chr2:208994621-208995421	U2OS	brain:	n/a	n/a
20	TCF12	chr2:208994726-208995231	SK-N-SH	brain:	n/a	n/a
21	EP300	chr2:208994855-208995453	HepG2	liver:	n/a	n/a
22	CEBPB	chr2:208994773-208995164	Hela-S3	cervix:	n/a	chr2:208994983-208994994
23	EP300	chr2:208994656-208995194	SK-N-SH_RA	brain:	n/a	n/a
24	HDAC2	chr2:208994881-208995431	HepG2	liver:	n/a	n/a
25	RAD21	chr2:208994741-208995112	SK-N-SH_RA	brain:	n/a	n/a
26	EP300	chr2:208994534-208995224	SK-N-SH	brain:	n/a	n/a
27	PBX3	chr2:208994623-208995248	SK-N-SH	brain:	n/a	n/a
28	GATA3	chr2:208994411-208995438	SK-N-SH	brain:	n/a	chr2:208995025-208995032 chr2:208995025-208995032 chr2:208995021-208995037 chr2:208995018-208995039 chr2:208995024-208995032 chr2:208995025-208995032
29	YY1	chr2:208995085-208995449	HepG2	liver:	n/a	n/a
30	TCF12	chr2:208994598-208995349	SK-N-SH	brain:	n/a	n/a
31	MBD4	chr2:208994820-208995538	HepG2	liver:	n/a	n/a
32	BHLHE40	chr2:208994968-208995359	HepG2	liver:	n/a	n/a
33	KAP1	chr2:208994852-208995365	HEK293	kidney:	n/a	n/a
34	FOSL2	chr2:208994742-208995467	HepG2	liver:	n/a	chr2:208994932-208994942 chr2:208994932-208994942 chr2:208994933-208994941
35	MBD4	chr2:208994716-208995528	HepG2	liver:	n/a	n/a
36	EP300	chr2:208994812-208995492	HepG2	liver:	n/a	n/a
37	PBX3	chr2:208994644-208995291	SK-N-SH	brain:	n/a	n/a
38	NFIC	chr2:208994668-208995461	HepG2	liver:	n/a	n/a
39	GATA2	chr2:208994417-208995366	SH-SY5Y	brain:	n/a	chr2:208995025-208995032 chr2:208995025-208995032 chr2:208995021-208995037 chr2:208995018-208995039 chr2:208995025-208995032
40	HEY1	chr2:208994971-208995435	HepG2	liver:	n/a	n/a
41	TBP	chr2:208994986-208995336	HepG2	liver:	n/a	n/a
42	POLR2A	chr2:208995062-208995235	HepG2	liver:	n/a	n/a
43	RCOR1	chr2:208994866-208995350	HepG2	liver:	n/a	n/a
44	HNF4A	chr2:208994777-208995523	HepG2	liver:	n/a	chr2:208994998-208995006 chr2:208995264-208995279 chr2:208994795-208994810 chr2:208994796-208994810 chr2:208994796-208994808 chr2:208994796-208994811
45	MYBL2	chr2:208994784-208995632	HepG2	liver:	n/a	n/a
46	FOSL2	chr2:208994627-208995199	SK-N-SH	brain:	n/a	chr2:208994932-208994942 chr2:208994932-208994942 chr2:208994933-208994941
47	GATA3	chr2:208994893-208995218	MCF-7	breast:	n/a	chr2:208995025-208995032 chr2:208995025-208995032 chr2:208995021-208995037 chr2:208995018-208995039 chr2:208995024-208995032 chr2:208995025-208995032
48	HNF4G	chr2:208994834-208995449	HepG2	liver:	n/a	chr2:208994998-208995006
49	TCF12	chr2:208994998-208995376	HepG2	liver:	n/a	n/a
50	GATA3	chr2:208994715-208995168	SH-SY5Y	brain:	n/a	chr2:208995025-208995032 chr2:208995025-208995032 chr2:208995021-208995037 chr2:208995018-208995039 chr2:208995024-208995032 chr2:208995025-208995032

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:208989109..208991585-chr2:208994453..208996077,2	K562	blood:

Variant related genes	Relation type
CRYGC	TF binding region
ENSG00000118231	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10932242	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13389772	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13406918	0.95[ASN][1000 genomes]
rs13418861	0.95[ASN][1000 genomes]
rs17538374	0.80[ASN][1000 genomes]
rs1869195	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2060867	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2060868	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305428	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2601476	0.91[ASN][1000 genomes]
rs2601482	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2854715	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2854716	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2854717	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34224231	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7423872	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7425722	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7560171	0.96[ASN][1000 genomes]
rs7593973	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs796286	0.82[CHB][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap]
rs796288	0.80[ASN][1000 genomes]
rs971493	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv875747	chr2:208990345-209042963	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv875748	chr2:208994399-209033557	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208989400-208999800	Weak transcription	Pancreas	Pancrea
2	chr2:208993400-209002200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:208994000-208998400	Enhancers	Fetal Intestine Large	intestine
4	chr2:208994200-208995200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:208994200-208995400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:208994200-208995400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr2:208994200-208996200	Enhancers	Duodenum Mucosa	Duodenum
8	chr2:208994200-208997000	Enhancers	HMEC	breast
9	chr2:208994200-208998400	Enhancers	Fetal Intestine Small	intestine
10	chr2:208994400-208995200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:208994400-208995400	Enhancers	Placenta	Placenta
12	chr2:208994400-208995800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr2:208994600-208995200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:208994600-208995200	Enhancers	NH-A	brain
15	chr2:208994600-208995400	Enhancers	NHEK	skin
16	chr2:208994600-208995600	Flanking Active TSS	HepG2	liver
17	chr2:208994600-208995800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:208994600-208996000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:208994600-208996200	Enhancers	Hela-S3	cervix
20	chr2:208994600-208999600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:208994600-209002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:208994800-208996000	Enhancers	Stomach Mucosa	stomach
23	chr2:208995000-208995400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr2:208995000-208997000	Enhancers	Ovary	ovary

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