Variant report

Variant	rs72887059
Chromosome Location	chr1:45477241-45477242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:113)
CpG islands
(count:0)
Chromatin interactive
region (count:38)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:113 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:45476650-45477303	A549	lung:	n/a	n/a
2	KAP1	chr1:45476798-45478446	HEK293	kidney:	n/a	chr1:45477407-45477416
3	MYC	chr1:45476508-45477273	K562	blood:	n/a	n/a
4	CBX3	chr1:45476780-45479180	K562	blood:	n/a	n/a
5	POLR2A	chr1:45476631-45477353	GM12878	blood:	n/a	n/a
6	MAFK	chr1:45476621-45478788	GM12878	blood:	n/a	chr1:45477404-45477414
7	TAF1	chr1:45476722-45477252	H1-neurons	neurons:	n/a	n/a
8	CUX1	chr1:45476970-45478744	K562	blood:	n/a	n/a
9	WRNIP1	chr1:45476928-45477266	GM12878	blood:	n/a	n/a
10	MAX	chr1:45476484-45477270	ECC-1	luminal epithelium:	n/a	n/a
11	HA-E2F1	chr1:45476136-45477334	MCF-7	breast:	n/a	chr1:45476451-45476462
12	EGR1	chr1:45476855-45477387	K562	blood:	n/a	n/a
13	SP1	chr1:45476694-45477297	A549	lung:	n/a	n/a
14	SIN3AK20	chr1:45475934-45478388	MCF-7	breast:	n/a	n/a
15	HCFC1	chr1:45476110-45478872	Hela-S3	cervix:	n/a	n/a
16	YY1	chr1:45476620-45477270	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr1:45476891-45477246	GM12892	blood:	n/a	n/a
18	TRIM28	chr1:45476753-45479128	K562	blood:	n/a	chr1:45477407-45477416
19	MAX	chr1:45476768-45477277	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:45476697-45477267	H1-neurons	neurons:	n/a	n/a
21	ARID3A	chr1:45477000-45477997	HepG2	liver:	n/a	n/a
22	ZC3H11A	chr1:45476885-45477301	K562	blood:	n/a	n/a
23	TEAD4	chr1:45476784-45478967	K562	blood:	n/a	n/a
24	ARID3A	chr1:45476969-45477374	K562	blood:	n/a	n/a
25	SMC3	chr1:45476129-45477249	Hela-S3	cervix:	n/a	n/a
26	NR2F2	chr1:45476833-45479943	K562	blood:	n/a	n/a
27	PML	chr1:45476592-45478310	GM12878	blood:	n/a	chr1:45477407-45477416
28	RUNX3	chr1:45476697-45477328	GM12878	blood:	n/a	n/a
29	GTF2F1	chr1:45476946-45477439	K562	blood:	n/a	n/a
30	EP300	chr1:45477031-45477313	K562	blood:	n/a	n/a
31	RFX5	chr1:45477004-45478023	HepG2	liver:	n/a	chr1:45477720-45477736
32	YY1	chr1:45476735-45477296	SK-N-SH_RA	brain:	n/a	n/a
33	POLR2A	chr1:45476546-45477391	GM12892	blood:	n/a	n/a
34	POLR2A	chr1:45476837-45477371	HepG2	liver:	n/a	n/a
35	ZNF143	chr1:45476872-45477266	K562	blood:	n/a	n/a
36	MAZ	chr1:45476045-45478868	IMR90	lung:	n/a	chr1:45477970-45477980 chr1:45477973-45477980
37	HEY1	chr1:45476780-45477460	K562	blood:	n/a	n/a
38	PML	chr1:45476824-45479538	K562	blood:	n/a	chr1:45477407-45477416
39	POLR2A	chr1:45476705-45477278	HUVEC	blood vessel:	n/a	n/a
40	SP1	chr1:45476731-45478191	A549	lung:	n/a	n/a
41	POLR2A	chr1:45476686-45477486	HepG2	liver:	n/a	n/a
42	TCF12	chr1:45476131-45477276	ECC-1	luminal epithelium:	n/a	chr1:45476977-45476984
43	MXI1	chr1:45475602-45477470	SK-N-SH	brain:	n/a	n/a
44	GATA1	chr1:45476796-45478942	PBDE	blood:	n/a	chr1:45477109-45477119 chr1:45477113-45477130
45	MAFK	chr1:45476871-45478019	Hela-S3	cervix:	n/a	chr1:45477404-45477414
46	RCOR1	chr1:45476894-45477252	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:45476625-45477262	SK-N-MC	brain:	n/a	n/a
48	MTA3	chr1:45476135-45478318	GM12878	blood:	n/a	n/a
49	PML	chr1:45476676-45477409	K562	blood:	n/a	n/a
50	HMGN3	chr1:45476158-45477455	K562	blood:	n/a	n/a

No data

(count:38 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45305082..45310090-chr1:45475264..45482808,8	K562	blood:
2	chr1:45477030..45479805-chr1:46047527..46050763,5	K562	blood:
3	chr1:45193444..45198675-chr1:45475617..45480324,16	K562	blood:
4	chr1:45269727..45273120-chr1:45475175..45479286,6	K562	blood:
5	chr1:45264279..45267905-chr1:45476139..45480748,9	K562	blood:
6	chr1:45239135..45244789-chr1:45475459..45482236,15	K562	blood:
7	chr1:45476252..45479466-chr1:46015891..46017851,3	K562	blood:
8	chr1:45471285..45474230-chr1:45476025..45477954,2	MCF-7	breast:
9	chr1:45476357..45485239-chr1:45761850..45773601,48	K562	blood:
10	chr1:45451300..45453679-chr1:45476530..45479236,3	MCF-7	breast:
11	chr1:45306981..45310503-chr1:45474976..45481200,7	K562	blood:
12	chr1:45449901..45454181-chr1:45475970..45480540,16	K562	blood:
13	chr1:45268954..45275189-chr1:45475024..45480055,7	K562	blood:
14	chr1:45476992..45480023-chr1:45798913..45801605,5	K562	blood:
15	chr1:45282320..45290015-chr1:45470338..45482903,45	K562	blood:
16	chr1:45284268..45287037-chr1:45476110..45479807,4	MCF-7	breast:
17	chr1:45194719..45198675-chr1:45474706..45481379,10	K562	blood:
18	chr1:45186675..45188755-chr1:45476881..45478812,3	MCF-7	breast:
19	chr1:45184334..45189303-chr1:45475138..45480545,18	K562	blood:
20	chr1:45455788..45461421-chr1:45474837..45478788,5	MCF-7	breast:
21	chr1:45283389..45288095-chr1:45474959..45480313,6	MCF-7	breast:
22	chr1:45239617..45241510-chr1:45476171..45478089,2	MCF-7	breast:
23	chr1:45240714..45243157-chr1:45476342..45480108,4	MCF-7	breast:
24	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
25	chr1:45194277..45197109-chr1:45476180..45479040,2	MCF-7	breast:
26	chr1:45476210..45477994-chr1:45804757..45807098,3	MCF-7	breast:
27	chr1:45476992..45479513-chr1:45797519..45802277,7	K562	blood:
28	chr1:45476953..45479637-chr1:45985604..45989189,5	K562	blood:
29	chr1:45239592..45244618-chr1:45476667..45480609,10	K562	blood:
30	chr1:45273315..45275597-chr1:45475668..45479411,4	K562	blood:
31	chr1:45475963..45478525-chr1:45804448..45806898,2	MCF-7	breast:
32	chr1:45476699..45479087-chr1:45821651..45824622,2	MCF-7	breast:
33	chr1:45264355..45267553-chr1:45476139..45481796,8	K562	blood:
34	chr1:45184334..45189289-chr1:45475449..45480431,12	K562	blood:
35	chr1:45476976..45478536-chr1:45986194..45987782,2	K562	blood:
36	chr1:45476853..45482658-chr1:45802506..45807966,11	K562	blood:
37	chr1:45476265..45486633-chr1:45761064..45774272,63	K562	blood:
38	chr1:45470053..45471669-chr1:45475976..45477628,2	MCF-7	breast:

No data

Variant related genes	Relation type
HECTD3	TF binding region
UROD	TF binding region
ENSG00000117425	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000268949	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000238945	Chromatin interaction
ENSG00000226499	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000202031	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11211065	0.87[AFR][1000 genomes]
rs12059608	0.81[AFR][1000 genomes]
rs12061569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12063958	0.87[AFR][1000 genomes]
rs12068434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073834	0.86[AFR][1000 genomes]
rs12083931	0.98[AFR][1000 genomes]
rs12084469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12086670	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12087439	0.88[AFR][1000 genomes]
rs12092185	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28848532	0.83[AFR][1000 genomes]
rs60060850	0.99[AFR][1000 genomes]
rs61027524	0.87[AFR][1000 genomes]
rs61498433	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61741088	1.00[AFR][1000 genomes]
rs6429555	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6682367	0.81[AFR][1000 genomes]
rs72885293	0.83[AFR][1000 genomes]
rs72887005	0.86[AFR][1000 genomes]
rs72887019	0.88[AFR][1000 genomes]
rs72887047	1.00[AFR][1000 genomes]
rs72887050	0.99[AFR][1000 genomes]
rs72887057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72887092	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7512020	0.97[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 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	chr1:45475400-45477600	Flanking Active TSS	Colonic Mucosa	Colon
2	chr1:45475600-45480400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:45475800-45478600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:45475800-45478800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr1:45475800-45479200	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr1:45476000-45478600	Active TSS	Aorta	Aorta
7	chr1:45476000-45479000	Active TSS	Ovary	ovary
8	chr1:45476400-45477600	Bivalent/Poised TSS	HepG2	liver
9	chr1:45476400-45478200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:45476400-45478600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:45476400-45478600	Active TSS	Lung	lung
12	chr1:45476400-45478800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr1:45476600-45478200	Active TSS	Fetal Muscle Trunk	muscle
14	chr1:45476600-45478600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:45476800-45478200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:45476800-45478400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:45477000-45477400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
18	chr1:45477000-45477600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:45477000-45477600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:45477000-45477600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr1:45477000-45477600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr1:45477000-45477600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:45477000-45477600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:45477000-45477600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:45477000-45477600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:45477000-45477600	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr1:45477000-45477600	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr1:45477000-45477600	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr1:45477000-45477600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:45477000-45477600	Flanking Active TSS	Fetal Kidney	kidney
31	chr1:45477000-45477600	Flanking Active TSS	Fetal Lung	lung
32	chr1:45477000-45477600	Flanking Active TSS	Gastric	stomach
33	chr1:45477000-45477600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr1:45477000-45477600	Flanking Active TSS	Stomach Mucosa	stomach
35	chr1:45477000-45477600	Flanking Active TSS	HSMMtube	muscle
36	chr1:45477000-45477600	Flanking Active TSS	NHDF-Ad	bronchial
37	chr1:45477000-45477800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:45477000-45477800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr1:45477000-45477800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr1:45477000-45477800	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr1:45477000-45477800	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr1:45477000-45477800	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr1:45477000-45477800	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr1:45477000-45477800	Flanking Active TSS	Fetal Stomach	stomach
45	chr1:45477000-45477800	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr1:45477000-45477800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr1:45477000-45477800	Flanking Active TSS	Dnd41	blood
48	chr1:45477000-45477800	Flanking Active TSS	GM12878-XiMat	blood
49	chr1:45477000-45477800	Flanking Active TSS	Hela-S3	cervix
50	chr1:45477000-45477800	Flanking Active TSS	HMEC	breast

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