Variant report

Variant	rs2070858
Chromosome Location	chr5:52778583-52778584
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	POLR2A	chr5:52778183-52779990	HepG2	liver:	n/a	n/a
2	CHD1	chr5:52773963-52779659	IMR90	lung:	n/a	chr5:52776596-52776606 chr5:52777700-52777710 chr5:52776601-52776611
3	SIN3A	chr5:52777671-52779208	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr5:52776262-52779138	IMR90	lung:	n/a	chr5:52776513-52776525 chr5:52776611-52776621
5	POLR2A	chr5:52775052-52780368	SK-N-SH	brain:	n/a	n/a
6	SIN3AK20	chr5:52778266-52778767	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAZ	chr5:52778356-52779439	HepG2	liver:	n/a	chr5:52778393-52778400
8	ZNF143	chr5:52778289-52779167	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3AK20	chr5:52778140-52778624	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr5:52778158-52778595	MCF-7	breast:	n/a	n/a
11	CTCF	chr5:52778188-52779711	SK-N-SH	brain:	n/a	n/a
12	MXI1	chr5:52775095-52779435	IMR90	lung:	n/a	n/a
13	MXI1	chr5:52778189-52779087	H1-hESC	embryonic stem cell:	n/a	n/a
14	CHD2	chr5:52778336-52779100	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr5:52778212-52778598	MCF-7	breast:	n/a	chr5:52778393-52778400
16	RAD21	chr5:52778408-52779176	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr5:52778197-52778982	H1-hESC	embryonic stem cell:	n/a	chr5:52778393-52778400
18	POLR2A	chr5:52774375-52780496	HepG2	liver:	n/a	n/a
19	MAX	chr5:52778189-52779116	H1-hESC	embryonic stem cell:	n/a	chr5:52778393-52778400
20	POLR2A	chr5:52778430-52779564	HepG2	liver:	n/a	n/a
21	PBX3	chr5:52778016-52778641	SK-N-SH	brain:	n/a	n/a
22	TBP	chr5:52778520-52779131	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr5:52778103-52779513	HepG2	liver:	n/a	n/a
24	MXI1	chr5:52777749-52779590	HepG2	liver:	n/a	n/a
25	CTCF	chr5:52778480-52778630	RPTEC	kidney:	n/a	n/a
26	CTCF	chr5:52778460-52778610	BJ	skin:	n/a	n/a
27	POLR2A	chr5:52778555-52779546	HepG2	liver:	n/a	n/a
28	HEY1	chr5:52778138-52779453	HepG2	liver:	n/a	n/a
29	RAD21	chr5:52778451-52779376	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr5:52774388-52779438	IMR90	lung:	n/a	n/a
31	CTCF	chr5:52778560-52778710	WI-38	lung:	n/a	n/a
32	REST	chr5:52778179-52778585	HepG2	liver:	n/a	n/a
33	MBD4	chr5:52778114-52778793	HepG2	liver:	n/a	n/a
34	MAX	chr5:52778125-52779634	HepG2	liver:	n/a	chr5:52778393-52778400
35	MAX	chr5:52777485-52778617	A549	lung:	n/a	chr5:52777853-52777862 chr5:52778393-52778400
36	CTBP2	chr5:52777774-52779265	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr5:52777549-52779232	NB4	blood:	n/a	chr5:52777853-52777862 chr5:52778393-52778400
38	RAD21	chr5:52778499-52779182	H1-hESC	embryonic stem cell:	n/a	n/a
39	MYBL2	chr5:52778042-52779612	HepG2	liver:	n/a	n/a
40	MAX	chr5:52778171-52779549	HepG2	liver:	n/a	chr5:52778393-52778400
41	POLR2A	chr5:52778449-52778893	MCF-7	breast:	n/a	n/a
42	MAX	chr5:52778152-52779138	H1-hESC	embryonic stem cell:	n/a	chr5:52778393-52778400
43	POLR2A	chr5:52778102-52779514	HepG2	liver:	n/a	n/a
44	HEY1	chr5:52777376-52779702	HepG2	liver:	n/a	n/a
45	BHLHE40	chr5:52778230-52779611	HepG2	liver:	n/a	n/a
46	MAZ	chr5:52775039-52779172	IMR90	lung:	n/a	chr5:52777853-52777862 chr5:52776181-52776191 chr5:52778393-52778400 chr5:52775968-52775978 chr5:52775515-52775525
47	MAX	chr5:52777658-52778700	SK-N-SH	brain:	n/a	chr5:52777853-52777862 chr5:52778393-52778400
48	RAD21	chr5:52778169-52779263	SK-N-SH	brain:	n/a	n/a
49	MAX	chr5:52778159-52778974	SK-N-SH	brain:	n/a	chr5:52778393-52778400
50	MYC	chr5:52777651-52779279	NB4	blood:	n/a	chr5:52777853-52777862 chr5:52778393-52778400

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52778566..52779397-chr5:53166578..53167566,3	MCF-7	breast:

Variant related genes	Relation type
FST	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1423560	0.96[ASN][1000 genomes]
rs2019033	0.84[AMR][1000 genomes]
rs2287925	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3797296	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806901	0.93[ASN][1000 genomes]
rs3891316	0.86[AFR][1000 genomes];0.84[AMR][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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52774200-52778800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr5:52774200-52778800	Active TSS	Osteobl	bone
3	chr5:52774200-52779000	Active TSS	Colon Smooth Muscle	Colon
4	chr5:52774200-52779200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr5:52774400-52778600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:52774400-52778600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr5:52774400-52778600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:52774400-52778600	Active TSS	Aorta	Aorta
9	chr5:52774400-52778800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:52774400-52778800	Active TSS	Hela-S3	cervix
11	chr5:52774400-52778800	Active TSS	HSMM	muscle
12	chr5:52774400-52778800	Active TSS	HSMMtube	muscle
13	chr5:52774400-52778800	Active TSS	NHDF-Ad	bronchial
14	chr5:52774400-52779000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr5:52774400-52779000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:52774400-52779000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:52774400-52779000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:52774400-52779000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:52774400-52779000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr5:52774400-52779000	Active TSS	Gastric	stomach
21	chr5:52774400-52779000	Active TSS	Psoas Muscle	Psoas
22	chr5:52774400-52779000	Active TSS	A549	lung
23	chr5:52774400-52779200	Active TSS	H9 Cell Line	embryonic stem cell
24	chr5:52774400-52779200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:52774400-52779200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:52774400-52779400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:52774600-52778600	Active TSS	NHLF	lung
28	chr5:52774600-52778800	Bivalent/Poised TSS	Fetal Stomach	stomach
29	chr5:52774600-52779200	Active TSS	Rectal Smooth Muscle	rectum
30	chr5:52774800-52778600	Active TSS	HMEC	breast
31	chr5:52775000-52778800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:52775200-52778800	Bivalent/Poised TSS	HepG2	liver
33	chr5:52775200-52779000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:52776600-52779400	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr5:52776800-52778600	Active TSS	Right Atrium	heart
36	chr5:52777000-52778600	Active TSS	Left Ventricle	heart
37	chr5:52777000-52778600	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr5:52777000-52778600	Active TSS	Stomach Smooth Muscle	stomach
39	chr5:52777000-52778600	Weak transcription	Spleen	Spleen
40	chr5:52777000-52778800	Active TSS	Ovary	ovary
41	chr5:52777000-52779000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr5:52777000-52779000	Bivalent/Poised TSS	Fetal Brain Female	brain
43	chr5:52777200-52778600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
44	chr5:52777200-52778800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:52777200-52778800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
46	chr5:52777200-52779000	Active TSS	Brain Cingulate Gyrus	brain
47	chr5:52777200-52779000	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr5:52777200-52779000	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr5:52777200-52779400	Active TSS	Fetal Kidney	kidney
50	chr5:52777400-52778600	Enhancers	Sigmoid Colon	Sigmoid Colon

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