Variant report

Variant	rs62310990
Chromosome Location	chr4:93226074-93226075
allele	C/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	MAX	chr4:93225888-93226991	ECC-1	luminal epithelium:	n/a	chr4:93226850-93226860
2	KAP1	chr4:93225772-93226119	U2OS	brain:	n/a	n/a
3	TBP	chr4:93225857-93227104	H1-hESC	embryonic stem cell:	n/a	n/a
4	KAP1	chr4:93225585-93227669	HEK293	kidney:	n/a	n/a
5	POLR2A	chr4:93225955-93226246	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr4:93225815-93227598	H1-neurons	neurons:	n/a	n/a
7	TEAD4	chr4:93225899-93226287	H1-hESC	embryonic stem cell:	n/a	chr4:93226114-93226123
8	GATA2	chr4:93224773-93227616	SH-SY5Y	brain:	n/a	chr4:93226221-93226228 chr4:93226217-93226233 chr4:93226214-93226235 chr4:93226221-93226228 chr4:93226221-93226228 chr4:93224832-93224840 chr4:93224829-93224842 chr4:93224830-93224842
9	ZBTB7A	chr4:93225838-93227146	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr4:93226065-93226148	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr4:93223600-93227920	H1-neurons	neurons:	n/a	chr4:93226854-93226864 chr4:93225065-93225078 chr4:93226409-93226422 chr4:93226881-93226888
12	POLR2A	chr4:93224616-93227654	H1-neurons	neurons:	n/a	n/a
13	CHD1	chr4:93225639-93226298	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr4:93225674-93227415	H1-hESC	embryonic stem cell:	n/a	chr4:93226850-93226860
15	CTBP2	chr4:93224813-93227536	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr4:93225716-93227236	H1-hESC	embryonic stem cell:	n/a	chr4:93226850-93226860
17	TCF7L2	chr4:93225655-93226706	HEK293	kidney:	n/a	n/a
18	E2F6	chr4:93225669-93227417	H1-hESC	embryonic stem cell:	n/a	chr4:93226850-93226859 chr4:93226568-93226578 chr4:93226935-93226950
19	SIN3A	chr4:93224656-93227528	H1-hESC	embryonic stem cell:	n/a	chr4:93224964-93224973

Variant related genes	Relation type
ENSG00000248511	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10009241	0.86[EUR][1000 genomes]
rs10012379	0.89[EUR][1000 genomes]
rs10015916	0.86[EUR][1000 genomes]
rs10032538	0.86[EUR][1000 genomes]
rs10516906	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13121565	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13123172	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150879	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1513462	0.86[EUR][1000 genomes]
rs1513467	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17238193	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17238679	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17317393	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17619771	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1877598	0.92[EUR][1000 genomes]
rs2175767	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28396937	0.90[EUR][1000 genomes]
rs28550894	0.86[EUR][1000 genomes]
rs34742978	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35214260	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35358234	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35924929	1.00[ASN][1000 genomes]
rs36116627	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36123040	0.87[EUR][1000 genomes]
rs62310971	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62310993	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62310994	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62311001	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6824860	0.86[EUR][1000 genomes]
rs6848132	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs951961	0.86[EUR][1000 genomes]
rs951962	0.86[EUR][1000 genomes]
rs9990511	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530154	chr4:92396539-93359983	Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv999701	chr4:92518040-93233556	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537180	chr4:92518040-93233556	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1009960	chr4:92747531-93389054	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv470056	chr4:92837584-93322977	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv461587	chr4:92837584-93376231	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv594866	chr4:92837584-93376231	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv948712	chr4:93007985-93740409	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv879603	chr4:93053028-93276174	ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv879604	chr4:93064187-93287744	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv830007	chr4:93101912-93317656	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv594868	chr4:93190198-93391251	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv998246	chr4:93198845-93350325	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	esv1835393	chr4:93222515-93276174	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:93224000-93228600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:93224200-93227800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr4:93224400-93226200	Active TSS	Fetal Brain Female	brain
4	chr4:93224400-93228400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr4:93224400-93229200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr4:93224600-93226600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
7	chr4:93224600-93227600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr4:93224600-93227600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:93224600-93227800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:93224600-93229600	Active TSS	Brain Cingulate Gyrus	brain
11	chr4:93224600-93229800	Active TSS	Brain Anterior Caudate	brain
12	chr4:93224800-93226200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:93224800-93226200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:93224800-93226200	Active TSS	Right Ventricle	heart
15	chr4:93224800-93226200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
16	chr4:93224800-93226200	Bivalent Enhancer	NHEK	skin
17	chr4:93224800-93226400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr4:93224800-93226400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:93224800-93226400	Enhancers	Pancreas	Pancrea
20	chr4:93224800-93226400	Bivalent Enhancer	HMEC	breast
21	chr4:93224800-93226600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
22	chr4:93224800-93227000	Active TSS	Fetal Brain Male	brain
23	chr4:93224800-93227200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:93224800-93227400	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr4:93224800-93227400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:93224800-93227400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr4:93224800-93227400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
28	chr4:93224800-93227600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:93224800-93227600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:93224800-93227600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:93224800-93227600	Active TSS	Aorta	Aorta
32	chr4:93224800-93227600	Active TSS	Brain Substantia Nigra	brain
33	chr4:93224800-93227600	Active TSS	Right Atrium	heart
34	chr4:93224800-93228000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr4:93224800-93228000	Active TSS	Brain Angular Gyrus	brain
36	chr4:93225000-93226200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
37	chr4:93225000-93226200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:93225000-93226200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
39	chr4:93225000-93226400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:93225000-93226400	Active TSS	Left Ventricle	heart
41	chr4:93225000-93226600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:93225000-93227200	Bivalent Enhancer	Lung	lung
43	chr4:93225200-93226400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:93225200-93226800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
45	chr4:93225400-93226200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
46	chr4:93225400-93226200	Bivalent Enhancer	Ovary	ovary
47	chr4:93225400-93226400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:93225400-93226600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
49	chr4:93225600-93226200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:93225600-93226200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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