Variant report

Variant	rs2288554
Chromosome Location	chr7:128095843-128095844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:453)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:453 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr7:128095480-128096445	H1-hESC	embryonic stem cell:	n/a	chr7:128095864-128095873
2	GATA3	chr7:128095186-128096676	A549	lung:	n/a	n/a
3	SIX5	chr7:128095393-128095979	A549	lung:	n/a	n/a
4	TAF1	chr7:128095541-128096283	HepG2	liver:	n/a	n/a
5	GATA1	chr7:128095281-128096096	PBDE	blood:	n/a	n/a
6	HCFC1	chr7:128095382-128096158	K562	blood:	n/a	n/a
7	E2F6	chr7:128095376-128096213	A549	lung:	n/a	chr7:128095864-128095873
8	POLR2A	chr7:128095427-128096319	GM18505	blood:	n/a	n/a
9	FOXP2	chr7:128095663-128096079	PFSK-1	brain:	n/a	n/a
10	BCLAF1	chr7:128095442-128096405	GM12878	blood:	n/a	n/a
11	HDAC2	chr7:128095521-128095975	K562	blood:	n/a	chr7:128095865-128095874
12	REST	chr7:128095535-128096529	A549	lung:	n/a	n/a
13	E2F4	chr7:128095796-128096082	GM12878	blood:	n/a	chr7:128095864-128095873
14	TCF7L2	chr7:128095603-128096255	HCT-116	colon:	n/a	n/a
15	TBP	chr7:128095568-128096100	HepG2	liver:	n/a	n/a
16	ARID3A	chr7:128095715-128096015	HepG2	liver:	n/a	n/a
17	YY1	chr7:128095526-128096116	K562	blood:	n/a	n/a
18	POLR2A	chr7:128095460-128096426	A549	lung:	n/a	n/a
19	POLR2A	chr7:128095519-128096322	MCF-7	breast:	n/a	n/a
20	POLR2A	chr7:128095287-128096377	GM12878	blood:	n/a	n/a
21	POLR2A	chr7:128095542-128096191	HUVEC	blood vessel:	n/a	n/a
22	EP300	chr7:128095562-128095975	SK-N-SH_RA	brain:	n/a	n/a
23	MYC	chr7:128095650-128096053	K562	blood:	n/a	n/a
24	POLR2A	chr7:128095502-128096213	H1-neurons	neurons:	n/a	n/a
25	PAX5	chr7:128095397-128096203	GM12878	blood:	n/a	chr7:128095864-128095873
26	POU2F2	chr7:128095496-128096125	GM12891	blood:	n/a	n/a
27	POLR2A	chr7:128095330-128096292	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr7:128095161-128096213	HepG2	liver:	n/a	n/a
29	ZKSCAN1	chr7:128095446-128096075	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr7:128095397-128096226	PBDE	blood:	n/a	n/a
31	TCF12	chr7:128095056-128096481	A549	lung:	n/a	n/a
32	BCLAF1	chr7:128095455-128096137	GM12878	blood:	n/a	n/a
33	FOXA1	chr7:128095548-128095935	T-47D	breast:	n/a	n/a
34	REST	chr7:128095239-128096660	A549	lung:	n/a	n/a
35	GABPA	chr7:128095586-128096080	A549	lung:	n/a	chr7:128095860-128095874 chr7:128095863-128095874 chr7:128095865-128095874
36	POLR2A	chr7:128095518-128096189	K562	blood:	n/a	n/a
37	POLR2A	chr7:128095194-128096415	SK-N-SH	brain:	n/a	n/a
38	BACH1	chr7:128095348-128096367	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr7:128095449-128096217	ECC-1	luminal epithelium:	n/a	n/a
40	MAX	chr7:128095233-128096654	Hela-S3	cervix:	n/a	n/a
41	MYC	chr7:128095703-128095993	HUVEC	blood vessel:	n/a	n/a
42	PML	chr7:128095503-128096196	MCF-7	breast:	n/a	chr7:128095716-128095725
43	NRF1	chr7:128095661-128096054	K562	blood:	n/a	chr7:128095860-128095874 chr7:128095863-128095874 chr7:128095863-128095874 chr7:128095865-128095874
44	HCFC1	chr7:128095159-128096613	Hela-S3	cervix:	n/a	n/a
45	IRF4	chr7:128095450-128095894	GM12878	blood:	n/a	n/a
46	TAF1	chr7:128095566-128096106	PFSK-1	brain:	n/a	n/a
47	MAX	chr7:128095672-128096361	HepG2	liver:	n/a	n/a
48	POLR2A	chr7:128095492-128096111	GM12891	blood:	n/a	n/a
49	POLR2A	chr7:128095456-128096220	GM19193	blood:	n/a	n/a
50	CTCF	chr7:128095774-128096020	Spleen_OC	spleen:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:128095158..128096724-chr7:128104393..128107346,2	K562	blood:
2	chr6:30583338..30586020-chr7:128094975..128097321,2	MCF-7	breast:
3	chr7:128066135..128077193-chr7:128094256..128102719,54	MCF-7	breast:
4	chr7:128047161..128050830-chr7:128093884..128097132,5	K562	blood:
5	chr7:128094511..128096087-chr7:128168839..128171295,2	K562	blood:
6	chr17:57695760..57698174-chr7:128094723..128097065,2	MCF-7	breast:
7	chr7:5567965..5570019-chr7:128094692..128097449,2	MCF-7	breast:
8	chr7:128082541..128090035-chr7:128090151..128101015,22	MCF-7	breast:
9	chr2:239335039..239335745-chr7:128095242..128095893,2	Hela-S3	cervix:
10	chr7:128095000..128097525-chr7:128170265..128171989,2	MCF-7	breast:
11	chr7:128047161..128050572-chr7:128094387..128098790,7	K562	blood:
12	chr7:128049232..128052115-chr7:128095566..128097196,2	MCF-7	breast:
13	chr7:127981540..127985237-chr7:128094279..128097407,4	K562	blood:
14	chr5:179050145..179051089-chr7:128095365..128096266,2	HCT-116	colon:
15	chr7:128038192..128041556-chr7:128094283..128098008,3	MCF-7	breast:
16	chr7:128094286..128097516-chr7:128115288..128118444,4	K562	blood:

No data

Variant related genes	Relation type
HILPDA	TF binding region
ENSG00000240758	TF binding region
ENSG00000273184	TF binding region
ENSG00000273270	Chromatin interaction
ENSG00000242588	Chromatin interaction
ENSG00000238590	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000141367	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000106344	Chromatin interaction
ENSG00000165055	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000238750	Chromatin interaction
ENSG00000065802	Chromatin interaction
ENSG00000228700	Chromatin interaction
ENSG00000272601	Chromatin interaction
ENSG00000106348	Chromatin interaction
ENSG00000222894	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1048531	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10954185	0.90[AMR][1000 genomes]
rs11763326	0.87[AMR][1000 genomes]
rs11764599	0.82[AMR][1000 genomes]
rs11766743	0.87[AMR][1000 genomes]
rs11769087	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11769168	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11771063	0.87[AMR][1000 genomes]
rs11771514	0.87[AMR][1000 genomes]
rs12532613	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12540762	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17627068	0.89[ASN][1000 genomes]
rs1864232	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2288550	0.87[AMR][1000 genomes]
rs35501542	0.87[AMR][1000 genomes]
rs3793164	0.87[AMR][1000 genomes]
rs4500030	0.89[ASN][1000 genomes]
rs4728114	0.82[ASN][1000 genomes]
rs55706726	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57124454	0.87[AMR][1000 genomes]
rs57715170	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58727049	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59027033	0.92[ASN][1000 genomes]
rs59665775	0.85[ASN][1000 genomes]
rs62481099	0.87[AMR][1000 genomes]
rs62481100	0.87[AMR][1000 genomes]
rs62481103	0.87[AMR][1000 genomes]
rs62481115	0.84[AMR][1000 genomes]
rs62481116	0.87[AMR][1000 genomes]
rs62481123	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62481124	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62481131	0.89[ASN][1000 genomes]
rs62481140	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv608401	chr7:128083454-128108776	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128093800-128096800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr7:128094200-128096200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr7:128094400-128096800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr7:128094400-128097400	Active TSS	Fetal Kidney	kidney
5	chr7:128094600-128096000	Weak transcription	Spleen	Spleen
6	chr7:128094600-128097000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr7:128094600-128097400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr7:128094800-128097000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:128094800-128097000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:128095000-128096000	Active TSS	Colonic Mucosa	Colon
11	chr7:128095000-128096200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr7:128095000-128096200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:128095000-128096800	Active TSS	Psoas Muscle	Psoas
14	chr7:128095000-128097000	Active TSS	Ovary	ovary
15	chr7:128095000-128097000	Active TSS	Placenta Amnion	Placenta Amnion
16	chr7:128095000-128097200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr7:128095200-128096400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:128095200-128096400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr7:128095200-128096600	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr7:128095200-128096600	Active TSS	Left Ventricle	heart
21	chr7:128095200-128096800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr7:128095200-128096800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:128095200-128097000	Active TSS	Esophagus	oesophagus
24	chr7:128095200-128097200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:128095400-128096000	Active TSS	Brain Germinal Matrix	brain
26	chr7:128095400-128096000	Weak transcription	Small Intestine	intestine
27	chr7:128095400-128096200	Active TSS	Liver	Liver
28	chr7:128095400-128096200	Active TSS	Brain Cingulate Gyrus	brain
29	chr7:128095400-128096200	Active TSS	Brain Hippocampus Middle	brain
30	chr7:128095400-128096200	Active TSS	Brain Substantia Nigra	brain
31	chr7:128095400-128096200	Active TSS	Lung	lung
32	chr7:128095400-128096200	Active TSS	Right Ventricle	heart
33	chr7:128095400-128096200	Active TSS	HepG2	liver
34	chr7:128095400-128096400	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr7:128095400-128096600	Active TSS	Aorta	Aorta
36	chr7:128095400-128096600	Active TSS	Brain Angular Gyrus	brain
37	chr7:128095400-128097200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:128095400-128097200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr7:128095400-128097200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr7:128095400-128097400	Active TSS	Brain Anterior Caudate	brain
41	chr7:128095600-128096000	Active TSS	Primary T cells fromperipheralblood	blood
42	chr7:128095600-128096000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr7:128095600-128096000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr7:128095600-128096000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:128095600-128096000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:128095600-128096200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr7:128095600-128096200	Active TSS	Primary monocytes fromperipheralblood	blood
48	chr7:128095600-128096200	Active TSS	Primary B cells from peripheral blood	blood
49	chr7:128095600-128096200	Active TSS	Primary T cells from cord blood	blood
50	chr7:128095600-128096200	Active TSS	Primary hematopoietic stem cells	blood

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