Variant report

Variant	rs1472944
Chromosome Location	chr18:9117562-9117563
allele	A/G
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	SMC3	chr18:9117337-9117611	GM12878	blood:	n/a	n/a
2	BCLAF1	chr18:9117169-9117668	GM12878	blood:	n/a	n/a
3	POLR2A	chr18:9117058-9117678	HUVEC	blood vessel:	n/a	n/a
4	FOS	chr18:9117244-9117657	MCF10A-Er-Src	breast:	n/a	chr18:9117423-9117434 chr18:9117401-9117412
5	IKZF1	chr18:9116541-9117739	GM12878	blood:	n/a	n/a
6	STAT3	chr18:9117386-9117584	MCF10A-Er-Src	breast:	n/a	n/a
7	FOSL2	chr18:9117260-9117778	SK-N-SH	brain:	n/a	n/a
8	CHD1	chr18:9117281-9117700	GM12878	blood:	n/a	n/a
9	FOSL2	chr18:9117253-9117758	A549	lung:	n/a	n/a
10	MYC	chr18:9117258-9117674	MCF10A-Er-Src	breast:	n/a	n/a
11	NR3C1	chr18:9117327-9117637	A549	lung:	n/a	n/a
12	JUND	chr18:9117236-9117639	Hela-S3	cervix:	n/a	chr18:9117423-9117434
13	RFX5	chr18:9117226-9117665	Hela-S3	cervix:	n/a	n/a
14	IRF1	chr18:9117407-9117665	K562	blood:	n/a	n/a
15	TBL1XR1	chr18:9117206-9117690	GM12878	blood:	n/a	n/a
16	FOSL2	chr18:9117259-9117573	MCF-7	breast:	n/a	n/a
17	PAX5	chr18:9117218-9117683	GM12891	blood:	n/a	chr18:9117548-9117567
18	FOS	chr18:9117184-9117717	HUVEC	blood vessel:	n/a	chr18:9117423-9117434 chr18:9117401-9117412
19	POLR2A	chr18:9117343-9117610	MCF10A-Er-Src	breast:	n/a	n/a
20	RCOR1	chr18:9117262-9117600	Hela-S3	cervix:	n/a	n/a
21	EBF1	chr18:9117260-9117743	GM12878	blood:	n/a	n/a
22	MAX	chr18:9117313-9117655	GM12878	blood:	n/a	n/a
23	PBX3	chr18:9117134-9117777	SK-N-SH	brain:	n/a	n/a
24	BHLHE40	chr18:9117248-9117689	GM12878	blood:	n/a	n/a
25	SIN3AK20	chr18:9117478-9117632	PFSK-1	brain:	n/a	n/a
26	PML	chr18:9117256-9117567	GM12878	blood:	n/a	n/a
27	PAX5	chr18:9117453-9117697	GM12892	blood:	n/a	chr18:9117548-9117567
28	NFIC	chr18:9116576-9117833	GM12878	blood:	n/a	n/a
29	POLR2A	chr18:9117109-9117631	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr18:9117440-9117603	HUVEC	blood vessel:	n/a	n/a
31	STAT5A	chr18:9117149-9117725	GM12878	blood:	n/a	n/a
32	POLR2A	chr18:9117151-9117814	MCF10A-Er-Src	breast:	n/a	n/a
33	IRF4	chr18:9117139-9117723	GM12878	blood:	n/a	n/a
34	BCL3	chr18:9117198-9117573	GM12878	blood:	n/a	n/a
35	FOSL2	chr18:9117226-9117617	HepG2	liver:	n/a	n/a
36	STAT3	chr18:9117367-9117585	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr18:9117476-9117664	GM12878	blood:	n/a	n/a
38	GATA3	chr18:9117168-9117795	SK-N-SH	brain:	n/a	n/a
39	FOS	chr18:9117223-9117697	MCF10A-Er-Src	breast:	n/a	chr18:9117423-9117434 chr18:9117401-9117412
40	POLR2A	chr18:9117262-9117729	GM12878	blood:	n/a	n/a
41	POLR2A	chr18:9116109-9117767	HepG2	liver:	n/a	n/a
42	MTA3	chr18:9116678-9117798	GM12878	blood:	n/a	n/a
43	RFX5	chr18:9117343-9117565	GM12878	blood:	n/a	n/a
44	CUX1	chr18:9117425-9117691	GM12878	blood:	n/a	n/a
45	SP1	chr18:9117099-9117734	HCT-116	colon:	n/a	n/a
46	EP300	chr18:9117233-9117613	SK-N-SH_RA	brain:	n/a	n/a
47	FOXA1	chr18:9117249-9117723	A549	lung:	n/a	n/a
48	FOS	chr18:9117222-9117672	MCF10A-Er-Src	breast:	n/a	chr18:9117423-9117434 chr18:9117401-9117412
49	TBP	chr18:9117290-9117612	GM12878	blood:	n/a	n/a
50	IRF4	chr18:9117084-9117713	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9117343..9120126-chr18:9132921..9134783,2	K562	blood:
2	chr18:9117343..9119164-chr18:9132921..9135865,2	K562	blood:
3	chr18:9116916..9118754-chr18:9136071..9139010,3	K562	blood:

Variant related genes	Relation type
ENSG00000263847	TF binding region
NDUFV2	TF binding region
ENSG00000101745	Chromatin interaction
ENSG00000266053	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11661711	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12607307	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4078337	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4148966	0.93[ASN][1000 genomes]
rs4148967	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4797356	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4798772	0.91[ASN][1000 genomes]
rs4798776	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4798778	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56046470	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6417048	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7504137	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7504603	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7505120	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs874250	0.81[ASN][1000 genomes]
rs906807	0.81[ASN][1000 genomes]
rs977581	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9945360	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9947027	0.94[EUR][1000 genomes]
rs9952006	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9966631	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064883	chr18:8709670-9133224	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv431971	chr18:9081185-9326852	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1056258	chr18:9094498-9181498	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv909364	chr18:9114096-9186684	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9104400-9130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:9106200-9123200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr18:9107000-9135200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr18:9107400-9135400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:9107600-9123200	Weak transcription	Thymus	Thymus
6	chr18:9107800-9134600	Weak transcription	Fetal Brain Male	brain
7	chr18:9108200-9123000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:9108200-9127200	Weak transcription	Fetal Brain Female	brain
9	chr18:9109600-9123200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr18:9110600-9118200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr18:9111200-9117600	Weak transcription	Fetal Lung	lung
12	chr18:9111200-9125400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr18:9111600-9126800	Weak transcription	Colonic Mucosa	Colon
14	chr18:9111800-9123400	Weak transcription	Fetal Stomach	stomach
15	chr18:9112000-9117800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr18:9112400-9118400	Enhancers	Liver	Liver
17	chr18:9113000-9119800	Enhancers	Brain Hippocampus Middle	brain
18	chr18:9113400-9118800	Genic enhancers	K562	blood
19	chr18:9114000-9118200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr18:9114000-9118400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr18:9114000-9119600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr18:9114000-9121000	Weak transcription	Fetal Muscle Leg	muscle
23	chr18:9114000-9123200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr18:9114000-9123400	Weak transcription	Fetal Intestine Small	intestine
25	chr18:9114000-9127400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr18:9114000-9130800	Weak transcription	Ovary	ovary
27	chr18:9114600-9118200	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr18:9114800-9118000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr18:9115400-9117800	Enhancers	A549	lung
30	chr18:9115400-9134600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr18:9115600-9119600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr18:9115600-9119800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr18:9115800-9118400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr18:9115800-9134800	Strong transcription	Dnd41	blood
35	chr18:9116000-9117600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr18:9116000-9117600	Genic enhancers	Primary B cells from cord blood	blood
37	chr18:9116000-9117800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr18:9116000-9119600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr18:9116200-9118800	Enhancers	Brain Angular Gyrus	brain
40	chr18:9116400-9117800	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr18:9116600-9117600	Enhancers	Primary T cells from cord blood	blood
42	chr18:9116600-9118600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr18:9116600-9118600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr18:9116600-9118800	Enhancers	Adipose Nuclei	Adipose
45	chr18:9116600-9118800	Enhancers	Brain Anterior Caudate	brain
46	chr18:9116600-9119000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr18:9116600-9119200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr18:9116600-9119400	Enhancers	Primary hematopoietic stem cells	blood
49	chr18:9116600-9119400	Enhancers	Stomach Mucosa	stomach
50	chr18:9116600-9119800	Enhancers	Brain Cingulate Gyrus	brain

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