Variant report

Variant	rs28364604
Chromosome Location	chr3:112360039-112360040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:197)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:197 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:112359734-112360334	K562	blood:	n/a	n/a
2	MAX	chr3:112358983-112360732	A549	lung:	n/a	chr3:112360464-112360473
3	POLR2A	chr3:112358726-112360545	SK-N-SH	brain:	n/a	n/a
4	RCOR1	chr3:112359872-112360245	K562	blood:	n/a	n/a
5	MAX	chr3:112358802-112360786	SK-N-SH	brain:	n/a	chr3:112360464-112360473
6	CEBPB	chr3:112358594-112360673	A549	lung:	n/a	chr3:112358750-112358761
7	POLR2A	chr3:112359738-112360225	A549	lung:	n/a	n/a
8	PBX3	chr3:112359710-112360326	SK-N-SH	brain:	n/a	n/a
9	PML	chr3:112359745-112360341	MCF-7	breast:	n/a	n/a
10	CTCF	chr3:112359722-112360097	K562	blood:	n/a	n/a
11	SIX5	chr3:112359766-112360577	A549	lung:	n/a	n/a
12	POLR2A	chr3:112359741-112360280	HCT-116	colon:	n/a	n/a
13	USF1	chr3:112359835-112360277	A549	lung:	n/a	n/a
14	POLR2A	chr3:112359596-112360338	K562	blood:	n/a	n/a
15	TCF12	chr3:112359737-112360287	A549	lung:	n/a	n/a
16	MAFK	chr3:112358924-112360416	Hela-S3	cervix:	n/a	chr3:112359917-112359932
17	MXI1	chr3:112359494-112360160	K562	blood:	n/a	n/a
18	POLR2A	chr3:112359825-112360166	A549	lung:	n/a	n/a
19	SP1	chr3:112358971-112360621	A549	lung:	n/a	chr3:112359997-112360007
20	MYC	chr3:112359916-112360147	K562	blood:	n/a	n/a
21	MAX	chr3:112359946-112360146	H1-hESC	embryonic stem cell:	n/a	n/a
22	GATA3	chr3:112358736-112360473	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr3:112359738-112360281	GM12892	blood:	n/a	n/a
24	GATA3	chr3:112359598-112360297	SK-N-SH	brain:	n/a	n/a
25	FOS	chr3:112359868-112360443	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr3:112359588-112360334	K562	blood:	n/a	n/a
27	POLR2A	chr3:112359830-112360201	A549	lung:	n/a	n/a
28	CTCF	chr3:112359900-112360050	HPAF	blood vessel:	n/a	n/a
29	TAF7	chr3:112359712-112360311	K562	blood:	n/a	n/a
30	SMC3	chr3:112359043-112360546	Hela-S3	cervix:	n/a	n/a
31	HCFC1	chr3:112359906-112360209	K562	blood:	n/a	n/a
32	ZBTB33	chr3:112359658-112360390	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr3:112359526-112360366	K562	blood:	n/a	n/a
34	JUND	chr3:112359855-112360355	H1-hESC	embryonic stem cell:	n/a	n/a
35	STAT3	chr3:112359868-112360182	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr3:112359590-112360239	K562	blood:	n/a	n/a
37	RFX5	chr3:112359075-112360492	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:112359734-112360198	GM12892	blood:	n/a	n/a
39	REST	chr3:112359772-112360149	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr3:112358884-112362166	IMR90	lung:	n/a	n/a
41	POLR2A	chr3:112359690-112360293	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:112358922-112360408	MCF10A-Er-Src	breast:	n/a	n/a
43	ARID3A	chr3:112360027-112360304	K562	blood:	n/a	n/a
44	POLR2A	chr3:112359762-112360285	HUVEC	blood vessel:	n/a	n/a
45	KAP1	chr3:112359019-112360794	HEK293	kidney:	n/a	n/a
46	POLR2A	chr3:112359675-112360278	GM12891	blood:	n/a	n/a
47	SP1	chr3:112359679-112360385	H1-hESC	embryonic stem cell:	n/a	chr3:112359997-112360007
48	POLR2A	chr3:112359801-112360275	HCT-116	colon:	n/a	n/a
49	BCLAF1	chr3:112359748-112360359	K562	blood:	n/a	n/a
50	POLR2A	chr3:112359641-112360383	HCT-116	colon:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:112359885..112361404-chr3:112367931..112369710,2	MCF-7	breast:
2	chr3:112358576..112361067-chr3:112520655..112523598,3	MCF-7	breast:
3	chr3:112289268..112293035-chr3:112358216..112361029,3	MCF-7	breast:
4	chr3:112359858..112360411-chr7:100025644..100026612,2	Hela-S3	cervix:
5	chr3:112358478..112360877-chr3:112708365..112711089,3	MCF-7	breast:
6	chr3:112358855..112360949-chr3:112737036..112738900,2	K562	blood:
7	chr3:112354638..112357493-chr3:112357624..112362114,5	K562	blood:
8	chr3:112358680..112360592-chr3:112737016..112739347,2	MCF-7	breast:
9	chr3:112357856..112364091-chr3:112692717..112699765,9	MCF-7	breast:
10	chr3:112278745..112284115-chr3:112357887..112361363,11	MCF-7	breast:
11	chr3:112358506..112363260-chr3:112706755..112711649,8	K562	blood:
12	chr3:112279172..112282504-chr3:112358640..112361542,6	MCF-7	breast:
13	chr3:112358697..112360499-chr3:112735766..112739410,3	MCF-7	breast:
14	chr3:112279230..112282432-chr3:112358112..112361671,5	K562	blood:
15	chr3:112359721..112360525-chr9:125675165..125676110,2	Hela-S3	cervix:
16	chr17:48784635..48785585-chr3:112359690..112360504,2	Hela-S3	cervix:
17	chr19:19030312..19031078-chr3:112359710..112360246,2	Hela-S3	cervix:
18	chr3:112359608..112361417-chr3:113001269..113003641,2	MCF-7	breast:
19	chr3:112011328..112014210-chr3:112359098..112361496,2	MCF-7	breast:
20	chr3:112357488..112363507-chr3:112707947..112711649,7	K562	blood:
21	chr3:112279230..112281440-chr3:112358030..112362501,6	K562	blood:
22	chr3:112358718..112361602-chr3:112709202..112711684,5	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC80	TF binding region
ENSG00000091986	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000172139	Chromatin interaction
ENSG00000240057	Chromatin interaction
ENSG00000154945	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000242770	Chromatin interaction
ENSG00000105671	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000144857	Chromatin interaction
ENSG00000163608	Chromatin interaction
ENSG00000186130	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000163606	Chromatin interaction
ENSG00000272844	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12634229	0.82[ASN][1000 genomes]
rs16859897	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16859911	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16859916	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28364588	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364589	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56721759	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59902026	0.85[AFR][1000 genomes]
rs7640793	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112354000-112360600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:112355800-112360200	Active TSS	Rectal Mucosa Donor 31	rectum
3	chr3:112356000-112360600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr3:112357200-112360400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:112357200-112361000	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr3:112358000-112360400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:112358000-112360400	Active TSS	Right Ventricle	heart
8	chr3:112358400-112360400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:112358600-112360200	Active TSS	Brain Hippocampus Middle	brain
10	chr3:112358600-112360200	Active TSS	Colon Smooth Muscle	Colon
11	chr3:112358600-112360400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:112358600-112360400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:112358600-112360400	ZNF genes & repeats	Fetal Brain Male	brain
14	chr3:112358600-112360400	Active TSS	HSMM	muscle
15	chr3:112358600-112360600	Flanking Active TSS	HUVEC	blood vessel
16	chr3:112358600-112361800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:112358600-112363200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:112358600-112365400	Weak transcription	Lung	lung
19	chr3:112358800-112360200	Active TSS	Fetal Stomach	stomach
20	chr3:112358800-112360200	Active TSS	NHLF	lung
21	chr3:112358800-112360400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:112358800-112360400	Active TSS	Ovary	ovary
23	chr3:112358800-112360400	Active TSS	Right Atrium	heart
24	chr3:112358800-112360400	Active TSS	NHDF-Ad	bronchial
25	chr3:112358800-112363200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:112359000-112360200	Active TSS	Aorta	Aorta
27	chr3:112359000-112360200	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr3:112359000-112360400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:112359000-112360400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:112359000-112360400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:112359000-112360400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:112359000-112361200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:112359000-112363600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr3:112359200-112360200	Active TSS	Fetal Lung	lung
35	chr3:112359200-112360200	Active TSS	A549	lung
36	chr3:112359200-112360600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr3:112359200-112360600	Flanking Active TSS	Fetal Heart	heart
38	chr3:112359200-112361200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:112359200-112361200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:112359400-112360200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:112359400-112360200	Enhancers	Stomach Mucosa	stomach
42	chr3:112359400-112360400	Active TSS	Left Ventricle	heart
43	chr3:112359400-112360600	Enhancers	K562	blood
44	chr3:112359400-112361000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr3:112359400-112361000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr3:112359400-112363200	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr3:112359600-112360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:112359600-112360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:112359600-112360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:112359600-112360400	Bivalent/Poised TSS	Fetal Intestine Small	intestine

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