Variant report

Variant	rs28364588
Chromosome Location	chr3:112360454-112360455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:49)
CpG islands
(count:61)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:49 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:112358983-112360732	A549	lung:	n/a	chr3:112360464-112360473
2	POLR2A	chr3:112358726-112360545	SK-N-SH	brain:	n/a	n/a
3	MAX	chr3:112358802-112360786	SK-N-SH	brain:	n/a	chr3:112360464-112360473
4	CEBPB	chr3:112358594-112360673	A549	lung:	n/a	chr3:112358750-112358761
5	SIX5	chr3:112359766-112360577	A549	lung:	n/a	n/a
6	SP1	chr3:112358971-112360621	A549	lung:	n/a	chr3:112359997-112360007
7	GATA3	chr3:112358736-112360473	SK-N-SH	brain:	n/a	n/a
8	SMC3	chr3:112359043-112360546	Hela-S3	cervix:	n/a	n/a
9	YY1	chr3:112360254-112360603	SK-N-SH_RA	brain:	n/a	n/a
10	RFX5	chr3:112359075-112360492	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr3:112360400-112360550	HCPEpiC	choroid plexus:	n/a	n/a
12	POLR2A	chr3:112358884-112362166	IMR90	lung:	n/a	n/a
13	KAP1	chr3:112359019-112360794	HEK293	kidney:	n/a	n/a
14	NFIC	chr3:112358938-112360494	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr3:112359338-112360524	HUVEC	blood vessel:	n/a	n/a
16	MAX	chr3:112359086-112360463	A549	lung:	n/a	n/a
17	YY1	chr3:112360269-112360590	SK-N-SH_RA	brain:	n/a	n/a
18	GTF2F1	chr3:112359840-112360553	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr3:112359056-112360566	HUVEC	blood vessel:	n/a	n/a
20	TCF12	chr3:112358932-112360699	A549	lung:	n/a	n/a
21	SIN3AK20	chr3:112359090-112360526	SK-N-SH	brain:	n/a	n/a
22	EP300	chr3:112359603-112360460	A549	lung:	n/a	n/a
23	EP300	chr3:112359670-112360468	A549	lung:	n/a	n/a
24	FOSL2	chr3:112358894-112360538	A549	lung:	n/a	n/a
25	TCF12	chr3:112358661-112360765	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr3:112359494-112360565	HEK293	kidney:	n/a	n/a
27	MYC	chr3:112359621-112360545	MCF10A-Er-Src	breast:	n/a	chr3:112360464-112360473
28	POLR2A	chr3:112359231-112360457	HUVEC	blood vessel:	n/a	n/a
29	TAF1	chr3:112360272-112360542	SK-N-SH	brain:	n/a	n/a
30	SIX5	chr3:112359236-112360671	A549	lung:	n/a	n/a
31	POLR2A	chr3:112359410-112360523	H1-hESC	embryonic stem cell:	n/a	n/a
32	TBP	chr3:112359083-112360502	Hela-S3	cervix:	n/a	n/a
33	ZNF143	chr3:112359578-112360473	K562	blood:	n/a	n/a
34	EP300	chr3:112359624-112360642	SK-N-SH	brain:	n/a	n/a
35	TCF12	chr3:112359626-112360466	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr3:112359172-112360524	ProgFib	skin:	n/a	n/a
37	POLR2A	chr3:112359664-112360535	H1-hESC	embryonic stem cell:	n/a	n/a
38	SETDB1	chr3:112359887-112360556	U2OS	brain:	n/a	n/a
39	POLR2A	chr3:112358943-112360903	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr3:112358908-112360532	HUVEC	blood vessel:	n/a	n/a
41	JUND	chr3:112359575-112360522	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr3:112358933-112360505	U87	brain:	n/a	n/a
43	PBX3	chr3:112359696-112360571	A549	lung:	n/a	n/a
44	GATA3	chr3:112358828-112360501	A549	lung:	n/a	n/a
45	BCL3	chr3:112358844-112360481	A549	lung:	n/a	n/a
46	YY1	chr3:112359132-112360636	SK-N-SH	brain:	n/a	n/a
47	MAFK	chr3:112358936-112360478	IMR90	lung:	n/a	chr3:112359917-112359932
48	POLR2A	chr3:112358933-112360511	U87	brain:	n/a	n/a
49	SP1	chr3:112358957-112360548	A549	lung:	n/a	chr3:112359997-112360007

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:112360446-112360496	CMK	blood:	n/a
2	chr3:112360446-112360496	NHDF-neo	bronchial:	n/a
3	chr3:112360446-112360496	HCT-116	colon:	n/a
4	chr3:112360446-112360496	PANC-1	pancreas:	n/a
5	chr3:112360446-112360496	HEK293	kidney:	embryo
6	chr3:112360446-112360496	HL-60	blood:	n/a
7	chr3:112360446-112360496	ECC-1	luminal epithelium:	n/a
8	chr3:112360446-112360496	GM12892	blood:	n/a
9	chr3:112360446-112360496	MCF-7	breast:	n/a
10	chr3:112360446-112360496	HepG2	liver:	n/a
11	chr3:112360446-112360496	U87	brain:	n/a
12	chr3:112360446-112360496	HMEC	breast:	n/a
13	chr3:112360446-112360496	NB4	blood:	n/a
14	chr3:112360446-112360496	K562	blood:	n/a
15	chr3:112360446-112360496	HNPCEpiC	eye:	n/a
16	chr3:112360446-112360496	HCM	heart:	n/a
17	chr3:112360446-112360496	IMR90	lung:	fetal
18	chr3:112360446-112360496	BJ	skin:	n/a
19	chr3:112360446-112360496	HIPEpiC	eye:	n/a
20	chr3:112360446-112360496	H1-hESC	embryonic stem cell:	embryo
21	chr3:112360446-112360496	T-47D	breast:	n/a
22	chr3:112360446-112360496	AG04449	skin:	fetal
23	chr3:112360446-112360496	LNCaP	prostate:	n/a
24	chr3:112360446-112360496	HCPEpiC	choroid plexus:	n/a
25	chr3:112360446-112360496	SK-N-SH_RA	brain:	n/a
26	chr3:112360446-112360496	NHBE	bronchial:	n/a
27	chr3:112360446-112360496	HRPEpiC	eye:	n/a
28	chr3:112360446-112360496	AG09319	gingival:	n/a
29	chr3:112360446-112360496	AG09309	skin:	n/a
30	chr3:112360446-112360496	GM19239	blood:	n/a
31	chr3:112360446-112360496	HRCEpiC	kidney:	n/a
32	chr3:112360446-112360496	SK-N-MC	brain:	n/a
33	chr3:112360446-112360496	BE2_C	brain:	n/a
34	chr3:112360446-112360496	SAEC	small airway:	n/a
35	chr3:112360446-112360496	SK-N-SH	brain:	n/a
36	chr3:112360446-112360496	PFSK-1	brain:	n/a
37	chr3:112360446-112360496	HPAEpiC	pulmonary alveolar:	n/a
38	chr3:112360446-112360496	AG10803	skin:	n/a
39	chr3:112360446-112360496	Hela-S3	cervix:	n/a
40	chr3:112360446-112360496	Hepatocyte	liver:	n/a
41	chr3:112360446-112360496	GM12891	blood:	n/a
42	chr3:112360446-112360496	Caco-2	colon:	n/a
43	chr3:112360446-112360496	HRE	kidney:	n/a
44	chr3:112360446-112360496	AoSMC	blood vessel:	n/a
45	chr3:112360446-112360496	NH-A	brain:	n/a
46	chr3:112360446-112360496	SKMC	muscle:	n/a
47	chr3:112360446-112360496	HEEpiC	esophagus:	n/a
48	chr3:112360446-112360496	HAEpiC	amniotic membrane:	n/a
49	chr3:112360446-112360496	PrEC	prostate:	n/a
50	chr3:112360446-112360496	GM12878	blood:	n/a

(count:20 , 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	chr3:112358478..112360877-chr3:112708365..112711089,3	MCF-7	breast:
5	chr3:112358855..112360949-chr3:112737036..112738900,2	K562	blood:
6	chr3:112354638..112357493-chr3:112357624..112362114,5	K562	blood:
7	chr3:112358680..112360592-chr3:112737016..112739347,2	MCF-7	breast:
8	chr3:112357856..112364091-chr3:112692717..112699765,9	MCF-7	breast:
9	chr3:112278745..112284115-chr3:112357887..112361363,11	MCF-7	breast:
10	chr3:112358506..112363260-chr3:112706755..112711649,8	K562	blood:
11	chr3:112279172..112282504-chr3:112358640..112361542,6	MCF-7	breast:
12	chr3:112358697..112360499-chr3:112735766..112739410,3	MCF-7	breast:
13	chr3:112279230..112282432-chr3:112358112..112361671,5	K562	blood:
14	chr3:112359721..112360525-chr9:125675165..125676110,2	Hela-S3	cervix:
15	chr17:48784635..48785585-chr3:112359690..112360504,2	Hela-S3	cervix:
16	chr3:112359608..112361417-chr3:113001269..113003641,2	MCF-7	breast:
17	chr3:112011328..112014210-chr3:112359098..112361496,2	MCF-7	breast:
18	chr3:112357488..112363507-chr3:112707947..112711649,7	K562	blood:
19	chr3:112279230..112281440-chr3:112358030..112362501,6	K562	blood:
20	chr3:112358718..112361602-chr3:112709202..112711684,5	MCF-7	breast:

No data

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

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10511317	1.00[AFR][1000 genomes]
rs1072896	1.00[AFR][1000 genomes]
rs12630906	1.00[AFR][1000 genomes]
rs12634199	1.00[AFR][1000 genomes]
rs12634229	0.82[ASN][1000 genomes]
rs12637057	1.00[AFR][1000 genomes]
rs12637953	1.00[AFR][1000 genomes]
rs13059364	1.00[AFR][1000 genomes]
rs13063173	1.00[AFR][1000 genomes]
rs13078401	1.00[AFR][1000 genomes]
rs13079599	1.00[AFR][1000 genomes]
rs13081265	1.00[AFR][1000 genomes]
rs13086960	1.00[AFR][1000 genomes]
rs13096943	1.00[AFR][1000 genomes]
rs16845068	1.00[AFR][1000 genomes]
rs16845073	1.00[AFR][1000 genomes]
rs16859758	1.00[AFR][1000 genomes]
rs16859849	1.00[AFR][1000 genomes]
rs16859890	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16859897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16859911	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16859916	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16859930	1.00[AFR][1000 genomes]
rs16859961	1.00[AFR][1000 genomes]
rs28364589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364604	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34080815	1.00[AFR][1000 genomes]
rs34541731	1.00[AFR][1000 genomes]
rs34829517	1.00[AFR][1000 genomes]
rs34889961	1.00[AFR][1000 genomes]
rs34949685	1.00[AFR][1000 genomes]
rs34962178	1.00[AFR][1000 genomes]
rs35263368	1.00[AFR][1000 genomes]
rs35526995	1.00[AFR][1000 genomes]
rs35931975	1.00[AFR][1000 genomes]
rs36045008	1.00[AFR][1000 genomes]
rs36153507	1.00[AFR][1000 genomes]
rs3736269	1.00[AFR][1000 genomes]
rs3773701	1.00[AFR][1000 genomes]
rs3773704	1.00[AFR][1000 genomes]
rs56721759	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59191788	1.00[AFR][1000 genomes]
rs60340975	1.00[AFR][1000 genomes]
rs60646325	1.00[AFR][1000 genomes]
rs60733172	1.00[AFR][1000 genomes]
rs66546764	1.00[AFR][1000 genomes]
rs66791711	1.00[AFR][1000 genomes]
rs67021100	1.00[AFR][1000 genomes]
rs71317506	1.00[AFR][1000 genomes]
rs71317507	1.00[AFR][1000 genomes]
rs71317508	1.00[AFR][1000 genomes]
rs73229350	1.00[AFR][1000 genomes]
rs73229353	1.00[AFR][1000 genomes]
rs7640793	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:85 , 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	chr3:112356000-112360600	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr3:112357200-112361000	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr3:112358600-112360600	Flanking Active TSS	HUVEC	blood vessel
5	chr3:112358600-112361800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:112358600-112363200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:112358600-112365400	Weak transcription	Lung	lung
8	chr3:112358800-112363200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:112359000-112361200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:112359000-112363600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:112359200-112360600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
12	chr3:112359200-112360600	Flanking Active TSS	Fetal Heart	heart
13	chr3:112359200-112361200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:112359200-112361200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:112359400-112360600	Enhancers	K562	blood
16	chr3:112359400-112361000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:112359400-112361000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr3:112359400-112363200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:112359600-112362800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:112359600-112365400	Weak transcription	Pancreas	Pancrea
21	chr3:112359800-112360800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:112359800-112361200	Enhancers	Placenta	Placenta
23	chr3:112359800-112361200	Enhancers	Fetal Thymus	thymus
24	chr3:112359800-112361200	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr3:112359800-112362000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr3:112359800-112362000	Weak transcription	Brain Anterior Caudate	brain
27	chr3:112359800-112362600	Weak transcription	Esophagus	oesophagus
28	chr3:112359800-112362800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr3:112359800-112363000	Enhancers	HMEC	breast
30	chr3:112359800-112363400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr3:112360000-112360600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr3:112360000-112360600	Flanking Active TSS	Fetal Kidney	kidney
33	chr3:112360000-112360600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:112360000-112360600	Flanking Active TSS	Hela-S3	cervix
35	chr3:112360000-112360600	Flanking Active TSS	NH-A	brain
36	chr3:112360000-112360600	Flanking Active TSS	NHEK	skin
37	chr3:112360000-112361000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:112360000-112361000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr3:112360000-112361000	Flanking Active TSS	HSMMtube	muscle
40	chr3:112360000-112361000	Flanking Active TSS	Osteobl	bone
41	chr3:112360000-112361200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:112360000-112361800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:112360200-112360600	Flanking Active TSS	Fetal Lung	lung
44	chr3:112360200-112360600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr3:112360200-112360800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:112360200-112360800	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr3:112360200-112360800	Enhancers	Psoas Muscle	Psoas
48	chr3:112360200-112361000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:112360200-112361000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr3:112360200-112361000	Flanking Active TSS	A549	lung

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