Variant report

Variant	rs1423560
Chromosome Location	chr5:52775762-52775763
allele	G/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	RCOR1	chr5:52775413-52775936	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	POLR2A	chr5:52775052-52780368	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr5:52775498-52775785	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:52774386-52777094	HepG2	liver:	n/a	n/a
6	MAZ	chr5:52775488-52776469	HepG2	liver:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525
7	TBP	chr5:52775130-52775966	HepG2	liver:	n/a	n/a
8	POLR2A	chr5:52775674-52776120	HepG2	liver:	n/a	n/a
9	RAD21	chr5:52775233-52775959	IMR90	lung:	n/a	n/a
10	E2F4	chr5:52775248-52776115	MCF10A-Er-Src	breast:	n/a	chr5:52775806-52775821 chr5:52775810-52775822
11	GATA3	chr5:52774106-52777467	SK-N-SH	brain:	n/a	chr5:52774928-52774936 chr5:52776733-52776741
12	MAX	chr5:52775297-52776857	A549	lung:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525
13	HA-E2F1	chr5:52775601-52776748	Hela-S3	cervix:	n/a	chr5:52775806-52775821
14	UBTF	chr5:52775481-52775945	K562	blood:	n/a	n/a
15	TEAD4	chr5:52775279-52776150	SK-N-SH	brain:	n/a	n/a
16	MXI1	chr5:52775095-52779435	IMR90	lung:	n/a	n/a
17	POLR2A	chr5:52775103-52775831	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr5:52775375-52775881	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr5:52775760-52775910	GM12865	blood:	n/a	n/a
20	ZNF143	chr5:52775402-52775948	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3AK20	chr5:52775339-52775762	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr5:52775291-52775968	Hela-S3	cervix:	n/a	n/a
23	E2F6	chr5:52775744-52775915	K562	blood:	n/a	chr5:52775806-52775821 chr5:52775810-52775822
24	TAF1	chr5:52775361-52776534	SK-N-SH	brain:	n/a	n/a
25	MAX	chr5:52775390-52776567	SK-N-SH	brain:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525
26	HEY1	chr5:52774155-52777346	HepG2	liver:	n/a	chr5:52776435-52776450 chr5:52776602-52776617 chr5:52774757-52774772
27	POLR2A	chr5:52774375-52780496	HepG2	liver:	n/a	n/a
28	CHD2	chr5:52775433-52775960	Hela-S3	cervix:	n/a	n/a
29	NFIC	chr5:52775149-52776398	SK-N-SH	brain:	n/a	n/a
30	YY1	chr5:52775413-52776163	HepG2	liver:	n/a	chr5:52776134-52776145
31	TAF1	chr5:52775334-52775807	Hela-S3	cervix:	n/a	n/a
32	TAF1	chr5:52775445-52776125	H1-hESC	embryonic stem cell:	n/a	n/a
33	CREB1	chr5:52775303-52776721	HepG2	liver:	n/a	n/a
34	POLR2A	chr5:52775579-52775828	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr5:52775412-52776147	A549	lung:	n/a	chr5:52775968-52775978 chr5:52775515-52775525
36	POLR2A	chr5:52775330-52775790	ProgFib	skin:	n/a	n/a
37	MXI1	chr5:52775617-52776848	HepG2	liver:	n/a	n/a
38	MAX	chr5:52775298-52776853	HepG2	liver:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525
39	PBX3	chr5:52775296-52776526	SK-N-SH	brain:	n/a	n/a
40	EP300	chr5:52775176-52777032	SK-N-SH	brain:	n/a	chr5:52775256-52775265 chr5:52775427-52775441 chr5:52775543-52775552 chr5:52776515-52776531 chr5:52775383-52775397
41	ZBTB7A	chr5:52775389-52776862	ECC-1	luminal epithelium:	n/a	chr5:52775986-52775995
42	E2F6	chr5:52775416-52776136	A549	lung:	n/a	chr5:52775806-52775821 chr5:52775810-52775822
43	HEY1	chr5:52775021-52777484	HepG2	liver:	n/a	chr5:52776435-52776450 chr5:52776602-52776617
44	TCF7L2	chr5:52775403-52775803	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr5:52774388-52779438	IMR90	lung:	n/a	n/a
46	POLR2A	chr5:52775379-52776130	HepG2	liver:	n/a	n/a
47	POLR2A	chr5:52775353-52776896	HepG2	liver:	n/a	n/a
48	MAX	chr5:52775312-52776542	SK-N-SH	brain:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525
49	PBX3	chr5:52775232-52776606	SK-N-SH	brain:	n/a	n/a
50	BACH1	chr5:52775685-52775828	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:56735383..56737636-chr5:52775178..52776995,2	MCF-7	breast:

Variant related genes	Relation type
FST	TF binding region
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2070858	0.96[ASN][1000 genomes]
rs2287925	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs31305	1.00[CEU][hapmap]
rs3797296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3806901	0.94[ASN][1000 genomes]
rs9986304	0.88[CHD][hapmap]

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	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
4	nsv328038	chr5:52772280-52777292	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	esv3412161	chr5:52775245-52777493	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52774200-52775800	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr5:52774200-52776600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr5:52774200-52776600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr5:52774200-52776600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr5:52774200-52776600	Active TSS	Ovary	ovary
6	chr5:52774200-52776600	Active TSS	Stomach Smooth Muscle	stomach
7	chr5:52774200-52776800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr5:52774200-52776800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr5:52774200-52776800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr5:52774200-52777200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:52774200-52777400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:52774200-52778200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:52774200-52778800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:52774200-52778800	Active TSS	Osteobl	bone
15	chr5:52774200-52779000	Active TSS	Colon Smooth Muscle	Colon
16	chr5:52774200-52779200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr5:52774400-52775800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
18	chr5:52774400-52776000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:52774400-52776600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:52774400-52776600	Active TSS	Muscle Satellite Cultured Cells	--
21	chr5:52774400-52776600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:52774400-52776600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:52774400-52776600	Active TSS	Esophagus	oesophagus
24	chr5:52774400-52776600	Active TSS	Pancreas	Pancrea
25	chr5:52774400-52776600	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr5:52774400-52776600	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr5:52774400-52776600	Active TSS	NH-A	brain
28	chr5:52774400-52778200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:52774400-52778400	Active TSS	Right Ventricle	heart
30	chr5:52774400-52778400	Bivalent/Poised TSS	Thymus	Thymus
31	chr5:52774400-52778600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:52774400-52778600	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr5:52774400-52778600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:52774400-52778600	Active TSS	Aorta	Aorta
35	chr5:52774400-52778800	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr5:52774400-52778800	Active TSS	Hela-S3	cervix
37	chr5:52774400-52778800	Active TSS	HSMM	muscle
38	chr5:52774400-52778800	Active TSS	HSMMtube	muscle
39	chr5:52774400-52778800	Active TSS	NHDF-Ad	bronchial
40	chr5:52774400-52779000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr5:52774400-52779000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:52774400-52779000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr5:52774400-52779000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:52774400-52779000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:52774400-52779000	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr5:52774400-52779000	Active TSS	Gastric	stomach
47	chr5:52774400-52779000	Active TSS	Psoas Muscle	Psoas
48	chr5:52774400-52779000	Active TSS	A549	lung
49	chr5:52774400-52779200	Active TSS	H9 Cell Line	embryonic stem cell
50	chr5:52774400-52779200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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