Variant report

Variant	rs28520978
Chromosome Location	chr4:645548-645549
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	GABPA	chr4:645281-645660	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:645185-645583	H1-hESC	embryonic stem cell:	n/a	n/a
3	TCF12	chr4:645066-645588	ECC-1	luminal epithelium:	n/a	n/a
4	ZNF143	chr4:645421-645592	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:644808..646339-chr4:648173..650037,2	K562	blood:
2	chr4:644054..646414-chr4:656838..659721,2	MCF-7	breast:
3	chr4:644162..647846-chr4:649268..652076,4	MCF-7	breast:

Variant related genes	Relation type
PDE6B	TF binding region
ENSG00000242686	Chromatin interaction
ENSG00000133256	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10021714	0.83[ASN][1000 genomes]
rs10023472	0.82[ASN][1000 genomes]
rs10027866	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10031745	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10033239	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28374488	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28438498	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28469188	0.83[EUR][1000 genomes]
rs28502612	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28504161	0.84[AFR][1000 genomes]
rs28568555	0.92[AFR][1000 genomes]
rs28588872	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28600205	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28630797	0.90[AFR][1000 genomes]
rs28711586	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3864131	0.89[AFR][1000 genomes]
rs3934459	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4505760	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60316402	0.83[AFR][1000 genomes]
rs67030464	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67376373	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71602496	0.92[AFR][1000 genomes]
rs72613108	0.82[ASN][1000 genomes]
rs72613109	0.89[ASN][1000 genomes]
rs9992641	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription 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
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv4194	chr4:635316-657212	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	esv3386118	chr4:645418-645598	Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:640400-648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:642200-652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:643000-646000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:643200-646200	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr4:643200-648200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:644400-646000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:644600-645800	Enhancers	Gastric	stomach
13	chr4:644600-646200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:644800-645800	Enhancers	Pancreas	Pancrea
15	chr4:645000-645600	Active TSS	Brain Anterior Caudate	brain
16	chr4:645000-645600	Bivalent/Poised TSS	HepG2	liver
17	chr4:645000-646000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:645000-648200	Weak transcription	Esophagus	oesophagus
19	chr4:645200-645600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
20	chr4:645200-645800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:645200-646600	Active TSS	Brain Substantia Nigra	brain
22	chr4:645400-645600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
23	chr4:645400-645600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:645400-645600	Active TSS	Brain Cingulate Gyrus	brain
25	chr4:645400-645600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
26	chr4:645400-645600	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr4:645400-645600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr4:645400-645800	Weak transcription	Brain Angular Gyrus	brain

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