Variant report

Variant	rs590277
Chromosome Location	chr18:11994258-11994259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr18:11994217-11996003	IMR90	lung:	n/a	chr18:11994937-11994946
2	TEAD4	chr18:11994223-11994825	HepG2	liver:	n/a	n/a
3	MAX	chr18:11994248-11995839	A549	lung:	n/a	chr18:11994937-11994946 chr18:11994809-11994819
4	POLR2A	chr18:11994227-11996555	HL-60	blood:	n/a	n/a
5	TCF12	chr18:11994151-11995669	A549	lung:	n/a	n/a
6	POLR2A	chr18:11993291-11997275	Hela-S3	cervix:	n/a	n/a
7	STAT3	chr18:11994190-11994708	MCF10A-Er-Src	breast:	n/a	chr18:11994412-11994420
8	POLR2A	chr18:11994186-11994542	A549	lung:	n/a	n/a
9	POLR2A	chr18:11994160-11997305	HL-60	blood:	n/a	n/a
10	POLR2A	chr18:11994178-11996104	HepG2	liver:	n/a	n/a
11	SP1	chr18:11994250-11995191	A549	lung:	n/a	chr18:11995049-11995058 chr18:11995045-11995059 chr18:11995044-11995053
12	CEBPB	chr18:11994228-11994770	A549	lung:	n/a	chr18:11994620-11994633
13	POLR2A	chr18:11993400-11998536	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr18:11994216-11994568	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:11994002..11996965-chr18:12008009..12011015,3	MCF-7	breast:
2	chr18:11992964..11995381-chr18:12038056..12040567,2	MCF-7	breast:
3	chr18:11979171..11983679-chr18:11993501..11995734,4	MCF-7	breast:
4	chr18:11978568..11983192-chr18:11993805..11998306,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP002414.1.1-4	chr18:11993987-11994371	ENSG00000266955.1

Variant related genes	Relation type
IMPA2	TF binding region
ENSG00000141401	Chromatin interaction
ENSG00000266995	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs3859296	0.90[ASN][1000 genomes]
rs58393627	0.94[ASN][1000 genomes]
rs588257	0.90[ASN][1000 genomes]
rs589247	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs590100	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs591061	0.89[ASN][1000 genomes]
rs592577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs604962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs605047	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs605636	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs605964	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606020	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606105	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs606370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606478	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs607200	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs622061	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs622246	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs636173	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs636300	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs638063	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs638125	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs649396	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs649713	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs650727	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs655790	0.95[ASN][1000 genomes]
rs666521	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs667798	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs668223	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs669838	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs682271	0.90[ASN][1000 genomes]
rs683190	0.90[ASN][1000 genomes]
rs684680	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982400-12005000	Weak transcription	Aorta	Aorta
2	chr18:11982600-11995600	Weak transcription	Primary T cells from cord blood	blood
3	chr18:11982600-11995800	Weak transcription	Thymus	Thymus
4	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
5	chr18:11984200-11994600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:11984400-11995000	Weak transcription	GM12878-XiMat	blood
7	chr18:11986000-11995600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr18:11986400-11994600	Weak transcription	Liver	Liver
9	chr18:11987200-11994800	Weak transcription	Right Atrium	heart
10	chr18:11988000-11995600	Weak transcription	K562	blood
11	chr18:11988600-11995200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr18:11989400-11994400	Enhancers	HepG2	liver
13	chr18:11989400-11994600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr18:11989600-11996400	Enhancers	Pancreas	Pancrea
15	chr18:11989800-11994600	Weak transcription	Left Ventricle	heart
16	chr18:11990000-11994400	Weak transcription	Colonic Mucosa	Colon
17	chr18:11990000-11994800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr18:11990200-11995200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr18:11990400-11994400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr18:11990400-11994400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr18:11990400-11994600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr18:11990400-11994600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr18:11990400-11994600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr18:11990600-11994600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr18:11990600-11994600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr18:11990600-11995800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr18:11990800-11994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr18:11990800-11994600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr18:11990800-11994600	Weak transcription	NHLF	lung
30	chr18:11990800-11994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr18:11990800-11994800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr18:11990800-11995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr18:11991000-11994400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr18:11991000-11994800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr18:11991000-11995200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr18:11991000-11999200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr18:11991200-11994400	Weak transcription	Fetal Lung	lung
38	chr18:11991200-11994800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr18:11991400-11994600	Strong transcription	Fetal Stomach	stomach
40	chr18:11991600-11994400	Weak transcription	Ovary	ovary
41	chr18:11991600-11994600	Weak transcription	Psoas Muscle	Psoas
42	chr18:11991600-11994800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr18:11991800-11994400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr18:11992000-11995000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr18:11992400-11994400	Weak transcription	Right Ventricle	heart
46	chr18:11992600-11995200	Weak transcription	Spleen	Spleen
47	chr18:11993200-11996600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:11993200-11996600	Enhancers	HSMMtube	muscle
49	chr18:11993200-11998000	Enhancers	Stomach Mucosa	stomach
50	chr18:11993200-11998400	Enhancers	Fetal Muscle Trunk	muscle

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