Variant report

Variant	rs2843019
Chromosome Location	chr1:120309158-120309159
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	HNF4G	chr1:120308894-120309451	HepG2	liver:	n/a	chr1:120309227-120309242 chr1:120309229-120309241
2	GATA3	chr1:120308942-120309399	T-47D	breast:	n/a	n/a
3	HEY1	chr1:120308862-120309558	HepG2	liver:	n/a	n/a
4	FOXA1	chr1:120308841-120309457	HepG2	liver:	n/a	chr1:120309152-120309164
5	MYBL2	chr1:120308907-120309469	HepG2	liver:	n/a	n/a
6	JUND	chr1:120309003-120309421	T-47D	breast:	n/a	n/a
7	HDAC2	chr1:120308738-120309446	HepG2	liver:	n/a	n/a
8	EP300	chr1:120308878-120309493	HepG2	liver:	n/a	n/a
9	JUND	chr1:120308801-120309425	HepG2	liver:	n/a	n/a
10	TBP	chr1:120309054-120309436	HepG2	liver:	n/a	n/a
11	FOXA2	chr1:120309032-120309375	A549	lung:	n/a	chr1:120309152-120309164
12	HDAC2	chr1:120308925-120309523	HepG2	liver:	n/a	n/a
13	NFIC	chr1:120308892-120309428	HepG2	liver:	n/a	n/a
14	FOXA2	chr1:120308881-120309482	HepG2	liver:	n/a	chr1:120309152-120309164
15	MAZ	chr1:120309104-120309424	HepG2	liver:	n/a	n/a
16	MBD4	chr1:120308922-120309465	HepG2	liver:	n/a	n/a
17	FOXA1	chr1:120309021-120309414	T-47D	breast:	n/a	chr1:120309152-120309164
18	TEAD4	chr1:120308825-120309469	HepG2	liver:	n/a	n/a
19	RAD21	chr1:120308966-120309453	HepG2	liver:	n/a	n/a
20	EP300	chr1:120308883-120309495	HepG2	liver:	n/a	n/a
21	FOXA1	chr1:120309090-120309389	T-47D	breast:	n/a	chr1:120309152-120309164
22	FOXA2	chr1:120308018-120309794	HepG2	liver:	n/a	chr1:120309152-120309164
23	RAD21	chr1:120308910-120309511	HepG2	liver:	n/a	n/a
24	HNF4A	chr1:120308986-120309443	HepG2	liver:	n/a	chr1:120309227-120309242 chr1:120309229-120309241
25	RCOR1	chr1:120308921-120309430	HepG2	liver:	n/a	n/a
26	GATA3	chr1:120308864-120309423	T-47D	breast:	n/a	n/a
27	TCF12	chr1:120309034-120309380	HepG2	liver:	n/a	n/a
28	EP300	chr1:120308943-120309472	T-47D	breast:	n/a	n/a
29	NFIC	chr1:120308819-120309582	HepG2	liver:	n/a	n/a
30	EP300	chr1:120308963-120309373	HepG2	liver:	n/a	n/a
31	FOXA2	chr1:120308952-120309462	A549	lung:	n/a	chr1:120309152-120309164
32	CEBPB	chr1:120308931-120309289	HepG2	liver:	n/a	n/a
33	USF1	chr1:120308998-120309221	HepG2	liver:	n/a	n/a
34	HNF4G	chr1:120308924-120309414	HepG2	liver:	n/a	chr1:120309227-120309242 chr1:120309229-120309241
35	HNF4A	chr1:120308917-120309464	HepG2	liver:	n/a	chr1:120309227-120309242 chr1:120309229-120309241
36	NR2F2	chr1:120308884-120309512	HepG2	liver:	n/a	n/a
37	MYBL2	chr1:120308457-120309580	HepG2	liver:	n/a	n/a
38	RXRA	chr1:120308968-120309391	HepG2	liver:	n/a	n/a
39	ARID3A	chr1:120308359-120309408	HepG2	liver:	n/a	n/a
40	FOXA1	chr1:120308885-120309459	HepG2	liver:	n/a	chr1:120309152-120309164
41	FOXA1	chr1:120308866-120309532	HepG2	liver:	n/a	chr1:120309152-120309164
42	ESR1	chr1:120308965-120309222	T-47D	breast:	n/a	n/a
43	JUND	chr1:120309111-120309386	HepG2	liver:	n/a	n/a
44	REST	chr1:120308971-120309484	HepG2	liver:	n/a	chr1:120309068-120309081
45	SMC3	chr1:120308923-120309406	HepG2	liver:	n/a	n/a
46	SP1	chr1:120308846-120309537	HepG2	liver:	n/a	n/a
47	FOXA1	chr1:120308837-120309526	HepG2	liver:	n/a	chr1:120309152-120309164

No.	Distal block	Cell Line	Cell type
1	chr1:120307608..120310232-chr1:120312392..120315286,2	MCF-7	breast:
2	chr1:120302494..120304014-chr1:120308491..120310237,2	K562	blood:
3	chr1:120305431..120308946-chr1:120308988..120311839,5	K562	blood:

Variant related genes	Relation type
HMGCS2	TF binding region
ENSG00000134240	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1441009	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs517237	0.83[AMR][1000 genomes]
rs532208	0.81[EUR][1000 genomes]
rs536662	0.83[EUR][1000 genomes]
rs619167	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs662924	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs673816	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120286800-120310000	Weak transcription	Psoas Muscle	Psoas
2	chr1:120291000-120310600	Weak transcription	Placenta	Placenta
3	chr1:120298200-120312200	Weak transcription	Right Ventricle	heart
4	chr1:120301000-120311600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:120307200-120309200	Weak transcription	Gastric	stomach
6	chr1:120307200-120309600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:120307200-120312000	Active TSS	Duodenum Mucosa	Duodenum
8	chr1:120308200-120309800	Enhancers	Stomach Mucosa	stomach
9	chr1:120308200-120311600	Active TSS	Rectal Smooth Muscle	rectum
10	chr1:120308400-120309800	Enhancers	Adipose Nuclei	Adipose
11	chr1:120308400-120309800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:120308400-120310000	Enhancers	Brain Substantia Nigra	brain
13	chr1:120308400-120310000	Flanking Active TSS	Fetal Intestine Large	intestine
14	chr1:120308400-120310400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:120308400-120310600	Enhancers	Brain Hippocampus Middle	brain
16	chr1:120308400-120311800	Active TSS	Colonic Mucosa	Colon
17	chr1:120308600-120309200	Enhancers	Fetal Heart	heart
18	chr1:120308600-120309600	Enhancers	Stomach Smooth Muscle	stomach
19	chr1:120308600-120309800	Enhancers	Brain Angular Gyrus	brain
20	chr1:120308600-120310200	Enhancers	Small Intestine	intestine
21	chr1:120308800-120309200	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr1:120308800-120309400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:120308800-120309400	Active TSS	Left Ventricle	heart
24	chr1:120308800-120309600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:120308800-120309800	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr1:120308800-120310000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:120308800-120310000	Enhancers	Colon Smooth Muscle	Colon
28	chr1:120308800-120310200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:120308800-120310200	Enhancers	Fetal Kidney	kidney
30	chr1:120308800-120310200	Flanking Active TSS	Fetal Stomach	stomach
31	chr1:120308800-120310200	Enhancers	Pancreas	Pancrea
32	chr1:120308800-120311200	Active TSS	Liver	Liver
33	chr1:120308800-120311800	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr1:120309000-120309200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:120309000-120309200	Enhancers	Esophagus	oesophagus
36	chr1:120309000-120309200	Bivalent Enhancer	NH-A	brain
37	chr1:120309000-120309400	Active TSS	Right Atrium	heart
38	chr1:120309000-120309400	Active TSS	HepG2	liver
39	chr1:120309000-120309600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:120309000-120309600	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr1:120309000-120309800	Enhancers	Brain Anterior Caudate	brain
42	chr1:120309000-120309800	Enhancers	Ovary	ovary
43	chr1:120309000-120312000	Enhancers	Fetal Lung	lung

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