Variant report

Variant	rs2287875
Chromosome Location	chr5:90676483-90676484
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:332)
CpG islands
(count:0)
Chromatin interactive
region (count:35)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:332 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:90675250-90680384	GM19099	blood:	n/a	n/a
2	ZNF143	chr5:90675754-90677295	GM12878	blood:	n/a	n/a
3	MAX	chr5:90675599-90677215	Hela-S3	cervix:	n/a	chr5:90676126-90676136
4	POLR2A	chr5:90675273-90680230	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr5:90675508-90680307	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr5:90674657-90680962	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr5:90675650-90680258	K562	blood:	n/a	n/a
8	MAX	chr5:90675621-90677034	MCF-7	breast:	n/a	chr5:90676126-90676136
9	TCF12	chr5:90675443-90677986	A549	lung:	n/a	n/a
10	MAX	chr5:90675647-90677149	SK-N-SH	brain:	n/a	chr5:90676126-90676136
11	SIN3AK20	chr5:90675582-90677416	MCF-7	breast:	n/a	n/a
12	CUX1	chr5:90676155-90677884	K562	blood:	n/a	n/a
13	POLR2A	chr5:90675390-90679948	GM19193	blood:	n/a	n/a
14	POLR2A	chr5:90674696-90680212	GM18505	blood:	n/a	n/a
15	CREB1	chr5:90675710-90677268	H1-hESC	embryonic stem cell:	n/a	n/a
16	REST	chr5:90675743-90676610	K562	blood:	n/a	chr5:90676125-90676138 chr5:90676125-90676138
17	CTCF	chr5:90676480-90676630	BE2_C	brain:	n/a	n/a
18	MAZ	chr5:90675738-90677109	HepG2	liver:	n/a	chr5:90676126-90676136
19	YY1	chr5:90675671-90677055	GM12892	blood:	n/a	chr5:90676133-90676142
20	EP300	chr5:90675725-90676532	SK-N-SH_RA	brain:	n/a	n/a
21	EP300	chr5:90676299-90678198	K562	blood:	n/a	chr5:90676915-90676931
22	POLR2A	chr5:90675666-90677220	ECC-1	luminal epithelium:	n/a	n/a
23	JUND	chr5:90675587-90677948	H1-hESC	embryonic stem cell:	n/a	chr5:90676132-90676141
24	MAX	chr5:90675671-90677021	SK-N-SH	brain:	n/a	chr5:90676126-90676136
25	PML	chr5:90675748-90677261	MCF-7	breast:	n/a	n/a
26	MAX	chr5:90676461-90677199	H1-hESC	embryonic stem cell:	n/a	n/a
27	MXI1	chr5:90675698-90680110	GM12878	blood:	n/a	chr5:90676872-90676887 chr5:90677625-90677634
28	REST	chr5:90676230-90676829	A549	lung:	n/a	n/a
29	POLR2A	chr5:90675791-90676901	A549	lung:	n/a	n/a
30	TBP	chr5:90675654-90677208	HepG2	liver:	n/a	n/a
31	GATA1	chr5:90675347-90681151	PBDE	blood:	n/a	chr5:90680794-90680801 chr5:90680794-90680803 chr5:90680794-90680801 chr5:90675376-90675387 chr5:90680567-90680576 chr5:90680794-90680801
32	CREB1	chr5:90675707-90676617	A549	lung:	n/a	n/a
33	POU2F2	chr5:90675628-90677246	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:90675447-90678156	K562	blood:	n/a	n/a
35	TCF7L2	chr5:90675735-90677053	HCT-116	colon:	n/a	n/a
36	CEBPD	chr5:90675586-90677260	K562	blood:	n/a	n/a
37	WRNIP1	chr5:90675699-90677231	GM12878	blood:	n/a	n/a
38	POLR2A	chr5:90675634-90677411	GM12892	blood:	n/a	n/a
39	CREB1	chr5:90675687-90676566	K562	blood:	n/a	n/a
40	POLR2A	chr5:90675711-90677196	Gliobla	brain:	n/a	n/a
41	POLR2A	chr5:90675603-90678075	K562	blood:	n/a	n/a
42	RUNX3	chr5:90675644-90677204	GM12878	blood:	n/a	n/a
43	MYC	chr5:90675606-90677202	NB4	blood:	n/a	chr5:90676126-90676136
44	POU2F2	chr5:90675755-90676486	GM12878	blood:	n/a	n/a
45	TAF1	chr5:90675618-90677351	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr5:90675461-90680144	HCT-116	colon:	n/a	n/a
47	POLR2A	chr5:90675604-90677139	H1-hESC	embryonic stem cell:	n/a	n/a
48	REST	chr5:90670312-90680754	H1-neurons	neurons:	n/a	chr5:90679211-90679220 chr5:90679214-90679227 chr5:90676125-90676138 chr5:90676125-90676138
49	EP300	chr5:90675607-90677164	H1-hESC	embryonic stem cell:	n/a	chr5:90676915-90676931
50	MAX	chr5:90675530-90680034	A549	lung:	n/a	chr5:90676126-90676136 chr5:90678077-90678086 chr5:90678078-90678085

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:167189231..167189842-chr5:90676068..90676590,2	Hela-S3	cervix:
2	chr5:90573090..90582351-chr5:90673821..90680716,23	K562	blood:
3	chr2:96873563..96874517-chr5:90676100..90676911,2	Hela-S3	cervix:
4	chr1:11333015..11333788-chr5:90676210..90676752,2	Hela-S3	cervix:
5	chr5:90574103..90582351-chr5:90673173..90681609,28	K562	blood:
6	chr5:43313326..43314007-chr5:90676210..90676872,2	Hela-S3	cervix:
7	chr17:78518411..78519347-chr5:90675922..90676719,2	NB4	blood:
8	chr5:90605667..90612137-chr5:90676262..90681561,13	K562	blood:
9	chr2:46843777..46844732-chr5:90676364..90676897,2	Hela-S3	cervix:
10	chr5:89705215..89707531-chr5:90675292..90676863,2	K562	blood:
11	chr17:57784385..57785314-chr5:90676010..90676689,2	Hela-S3	cervix:
12	chr5:90674940..90677586-chr5:98263946..98266440,2	K562	blood:
13	chr5:90675967..90676774-chr5:170814171..170814893,2	HCT-116	colon:
14	chr5:90676180..90677768-chr6:26156663..26159404,2	MCF-7	breast:
15	chr5:89705215..89707825-chr5:90675292..90676863,3	K562	blood:
16	chr15:65588150..65588692-chr5:90676476..90677085,2	Hela-S3	cervix:
17	chr5:89768584..89771978-chr5:90675764..90678297,3	K562	blood:
18	chr1:249132283..249132869-chr5:90676163..90676943,2	Hela-S3	cervix:
19	chr5:90574805..90578594-chr5:90673900..90681432,13	MCF-7	breast:
20	chr5:90607535..90610829-chr5:90673824..90679078,6	MCF-7	breast:
21	chr5:90512455..90524285-chr5:90673793..90683360,52	MCF-7	breast:
22	chr5:90607284..90611861-chr5:90674569..90683045,11	K562	blood:
23	chr5:90560937..90569122-chr5:90675177..90680484,12	K562	blood:
24	chr5:90674940..90679357-chr5:98262514..98267275,7	K562	blood:
25	chr5:90566473..90568664-chr5:90676122..90678989,3	K562	blood:
26	chr5:90607483..90611926-chr5:90672625..90681906,20	MCF-7	breast:
27	chr10:49892856..49893405-chr5:90676308..90676928,2	NB4	blood:
28	chr17:46125701..46126210-chr5:90676283..90676951,2	Hela-S3	cervix:
29	chr1:112938006..112938734-chr5:90676277..90676835,2	Hela-S3	cervix:
30	chr1:154192820..154193810-chr5:90676348..90676889,2	Hela-S3	cervix:
31	chr4:103749281..103749855-chr5:90676339..90677065,2	Hela-S3	cervix:
32	chr5:90512732..90524610-chr5:90674652..90682171,24	K562	blood:
33	chr5:90676216..90679010-chr5:94981409..94984145,2	K562	blood:
34	chr5:90513015..90523645-chr5:90674785..90682171,21	K562	blood:
35	chr5:90510244..90526030-chr5:90672528..90682389,53	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR98-10	chr5:90676164-90676741	NONHSAT102762
2	lnc-GPR98-10	chr5:90676169-90676741	NONHSAT102763

No data

Variant related genes	Relation type
ARRDC3	TF binding region
ENSG00000120942	Chromatin interaction
ENSG00000175449	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000248489	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000212930	Chromatin interaction
ENSG00000128815	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000234292	Chromatin interaction
ENSG00000151665	Chromatin interaction
ENSG00000271762	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000272205	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000181163	Chromatin interaction
ENSG00000141378	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000251093	Chromatin interaction
ENSG00000248323	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000141564	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000171161	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000199643	Chromatin interaction
ENSG00000112972	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000119878	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10514347	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10514348	0.81[ASN][1000 genomes]
rs10805875	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1133120	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16869743	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16869748	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16869750	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16876866	0.81[EUR][1000 genomes]
rs16878935	0.88[CEU][hapmap]
rs1807945	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2303130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146346	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56752631	0.81[EUR][1000 genomes]
rs73771404	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73771421	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73771425	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73773371	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73773374	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73773378	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9918274	0.94[EUR][1000 genomes];0.85[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	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 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	chr5:90673800-90679800	Active TSS	NHLF	lung
2	chr5:90673800-90680800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:90674000-90676600	Active TSS	Fetal Brain Female	brain
4	chr5:90674000-90680800	Active TSS	K562	blood
5	chr5:90674200-90680200	Active TSS	A549	lung
6	chr5:90674400-90680000	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr5:90674400-90680200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:90674400-90680200	Active TSS	Brain Cingulate Gyrus	brain
9	chr5:90674400-90680800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:90674600-90679600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:90674600-90679800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:90674600-90679800	Active TSS	Duodenum Mucosa	Duodenum
13	chr5:90674600-90679800	Active TSS	Fetal Muscle Leg	muscle
14	chr5:90674600-90679800	Active TSS	HSMMtube	muscle
15	chr5:90674600-90679800	Active TSS	NH-A	brain
16	chr5:90674600-90680000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr5:90674600-90680000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:90674600-90680000	Active TSS	Brain Substantia Nigra	brain
19	chr5:90674600-90680000	Active TSS	Ovary	ovary
20	chr5:90674600-90680200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:90674600-90680200	Active TSS	Placenta Amnion	Placenta Amnion
22	chr5:90674600-90680400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:90674600-90680600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:90674600-90680600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:90674600-90680600	Active TSS	Psoas Muscle	Psoas
26	chr5:90674600-90680600	Active TSS	Right Ventricle	heart
27	chr5:90674600-90680800	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr5:90674800-90679400	Active TSS	Primary T cells fromperipheralblood	blood
29	chr5:90674800-90679400	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr5:90674800-90679600	Active TSS	Fetal Thymus	thymus
31	chr5:90674800-90679600	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr5:90674800-90679800	Active TSS	Muscle Satellite Cultured Cells	--
33	chr5:90674800-90679800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr5:90674800-90679800	Active TSS	Fetal Lung	lung
35	chr5:90674800-90679800	Active TSS	Fetal Stomach	stomach
36	chr5:90674800-90679800	Active TSS	Stomach Smooth Muscle	stomach
37	chr5:90674800-90679800	Active TSS	Hela-S3	cervix
38	chr5:90674800-90680000	Active TSS	Aorta	Aorta
39	chr5:90674800-90680000	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr5:90674800-90680000	Active TSS	Fetal Kidney	kidney
41	chr5:90674800-90680000	Active TSS	HMEC	breast
42	chr5:90674800-90680200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:90674800-90680200	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr5:90674800-90680200	Active TSS	Fetal Intestine Small	intestine
45	chr5:90674800-90680200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr5:90674800-90680200	Active TSS	HSMM	muscle
47	chr5:90674800-90680200	Active TSS	NHDF-Ad	bronchial
48	chr5:90674800-90680800	Active TSS	Stomach Mucosa	stomach
49	chr5:90675000-90679400	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr5:90675000-90679400	Active TSS	Primary T helper naive cells from peripheral blood	blood

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