Variant report

Variant	rs58666702
Chromosome Location	chr2:99351854-99351855
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	EP300	chr2:99351189-99351885	HepG2	liver:	n/a	chr2:99351245-99351259 chr2:99351249-99351258 chr2:99351622-99351635 chr2:99351200-99351214
2	EP300	chr2:99351248-99351915	HepG2	liver:	n/a	chr2:99351249-99351258 chr2:99351622-99351635
3	TCF7L2	chr2:99351257-99351888	HepG2	liver:	n/a	chr2:99351637-99351651
4	NFIC	chr2:99351168-99351891	HepG2	liver:	n/a	n/a
5	FOXA1	chr2:99351215-99351899	HepG2	liver:	n/a	n/a
6	TEAD4	chr2:99351121-99351890	HepG2	liver:	n/a	n/a
7	NR2F2	chr2:99351289-99351882	HepG2	liver:	n/a	n/a
8	CREB1	chr2:99351272-99351910	HepG2	liver:	n/a	n/a
9	FOXA1	chr2:99351192-99351861	HepG2	liver:	n/a	n/a
10	MYBL2	chr2:99351152-99351886	HepG2	liver:	n/a	n/a
11	FOXA1	chr2:99351304-99351889	HepG2	liver:	n/a	n/a
12	FOXA2	chr2:99350962-99351892	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99346676..99348606-chr2:99349694..99353065,3	MCF-7	breast:

Variant related genes	Relation type
MGAT4A	TF binding region
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1016124	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10173832	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10174321	0.86[ASN][1000 genomes]
rs10177696	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194177	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10199267	0.88[EUR][1000 genomes]
rs10200288	0.87[ASN][1000 genomes]
rs10210711	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10460485	0.88[EUR][1000 genomes]
rs10496332	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123747	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123749	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123751	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11885883	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12471383	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12477450	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12615301	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12622931	0.88[EUR][1000 genomes]
rs12993424	0.89[ASN][1000 genomes]
rs13391483	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13391794	0.88[EUR][1000 genomes]
rs13392306	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13410406	0.88[EUR][1000 genomes]
rs13428808	0.87[EUR][1000 genomes]
rs1514916	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517681	0.89[ASN][1000 genomes]
rs1913621	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013983	0.89[ASN][1000 genomes]
rs28783173	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34521960	0.89[ASN][1000 genomes]
rs35477458	0.89[ASN][1000 genomes]
rs41445250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851150	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851153	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4851154	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5008045	0.82[EUR][1000 genomes]
rs60024860	0.88[EUR][1000 genomes]
rs6706340	0.82[EUR][1000 genomes]
rs6733957	0.88[EUR][1000 genomes]
rs6737760	0.88[EUR][1000 genomes]
rs6740656	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7420869	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558236	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7577636	0.88[EUR][1000 genomes]
rs7599792	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601040	0.82[EUR][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv535836	chr2:99329084-99353519	Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535837	chr2:99329084-99358356	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535838	chr2:99335416-99358356	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99348400-99352600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:99348400-99352600	Weak transcription	Small Intestine	intestine
3	chr2:99348400-99367000	Weak transcription	Esophagus	oesophagus
4	chr2:99348600-99353000	Weak transcription	NHEK	skin
5	chr2:99348600-99359200	Weak transcription	Aorta	Aorta
6	chr2:99348800-99352600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:99348800-99353000	Weak transcription	HMEC	breast
8	chr2:99348800-99360600	Weak transcription	Lung	lung
9	chr2:99349200-99357200	Enhancers	HepG2	liver
10	chr2:99349400-99352600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:99349400-99353800	Weak transcription	Pancreas	Pancrea
12	chr2:99349400-99355800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:99349800-99355200	Enhancers	Fetal Thymus	thymus
14	chr2:99350200-99352200	Weak transcription	Placenta	Placenta
15	chr2:99350400-99353200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:99350800-99352800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr2:99351200-99352400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:99351200-99355600	Enhancers	Primary T cells fromperipheralblood	blood
19	chr2:99351400-99352600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr2:99351400-99352800	Weak transcription	HUVEC	blood vessel
21	chr2:99351400-99355000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:99351400-99355800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:99351600-99353000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:99351600-99353000	Weak transcription	GM12878-XiMat	blood
25	chr2:99351600-99353200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:99351600-99353400	Enhancers	Dnd41	blood
27	chr2:99351600-99355000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:99351600-99355800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr2:99351800-99353000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:99351800-99353200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:99351800-99354400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:99351800-99354400	Weak transcription	Thymus	Thymus
33	chr2:99351800-99354600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr2:99351800-99355200	Weak transcription	Fetal Intestine Large	intestine
35	chr2:99351800-99355200	Weak transcription	Fetal Intestine Small	intestine
36	chr2:99351800-99355400	Enhancers	Primary T cells from cord blood	blood
37	chr2:99351800-99355800	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr2:99351800-99356200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr2:99351800-99356600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr2:99351800-99356600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr2:99351800-99360400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:99351800-99360600	Weak transcription	Rectal Mucosa Donor 31	rectum

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