Variant report

Variant	rs9964720
Chromosome Location	chr18:12377728-12377729
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	POLR2A	chr18:12377523-12377919	SK-N-MC	brain:	n/a	n/a
2	CTCF	chr18:12377600-12377750	NHLF	lung:	n/a	n/a
3	CTCF	chr18:12377682-12377826	NHEK	skin:	n/a	n/a
4	USF1	chr18:12377405-12377810	HepG2	liver:	n/a	chr18:12377654-12377670
5	YY1	chr18:12376661-12377894	K562	blood:	n/a	chr18:12376870-12376884 chr18:12376803-12376817 chr18:12377242-12377256 chr18:12377082-12377091
6	REST	chr18:12377507-12377903	SK-N-SH	brain:	n/a	n/a
7	FOXP2	chr18:12376742-12377940	PFSK-1	brain:	n/a	n/a
8	RCOR1	chr18:12377696-12377933	K562	blood:	n/a	n/a
9	MYC	chr18:12376126-12377946	K562	blood:	n/a	chr18:12376873-12376883 chr18:12377741-12377750
10	CTCF	chr18:12377620-12377770	HUVEC	blood vessel:	n/a	n/a
11	TEAD4	chr18:12377368-12378058	ECC-1	luminal epithelium:	n/a	chr18:12377784-12377793
12	CREB1	chr18:12376642-12377829	A549	lung:	n/a	n/a
13	CTCF	chr18:12377620-12377770	AG04450	lung:	n/a	n/a
14	CHD2	chr18:12377632-12378167	H1-hESC	embryonic stem cell:	n/a	n/a
15	SIN3AK20	chr18:12376391-12377931	K562	blood:	n/a	n/a
16	MAFF	chr18:12377566-12377918	HepG2	liver:	n/a	n/a
17	CTCF	chr18:12377600-12377750	HPAF	blood vessel:	n/a	n/a
18	MAFK	chr18:12377577-12378191	H1-hESC	embryonic stem cell:	n/a	chr18:12377740-12377750
19	CTCF	chr18:12377620-12377770	HEK293	kidney:	n/a	n/a
20	BHLHE40	chr18:12376078-12378109	K562	blood:	n/a	chr18:12377229-12377245 chr18:12377654-12377670 chr18:12376281-12376302
21	USF1	chr18:12377295-12377764	A549	lung:	n/a	chr18:12377654-12377670
22	CTCF	chr18:12377660-12377810	GM12865	blood:	n/a	n/a
23	MXI1	chr18:12376052-12377970	Hela-S3	cervix:	n/a	n/a
24	MYC	chr18:12377592-12377794	HUVEC	blood vessel:	n/a	chr18:12377741-12377750
25	MAX	chr18:12376261-12377907	K562	blood:	n/a	chr18:12376873-12376883 chr18:12377741-12377750
26	TCF3	chr18:12377632-12377802	GM12878	blood:	n/a	n/a
27	CTCF	chr18:12377620-12377770	GM12873	blood:	n/a	n/a
28	CTCF	chr18:12377600-12377750	SAEC	small airway:	n/a	n/a
29	BHLHE40	chr18:12377243-12377761	HepG2	liver:	n/a	chr18:12377654-12377670
30	ZNF143	chr18:12377110-12377933	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr18:12377660-12377810	AG09309	skin:	n/a	n/a
32	CTCF	chr18:12377682-12377849	GM19239	blood:	n/a	n/a
33	ELF1	chr18:12376438-12378069	GM12878	blood:	n/a	chr18:12376910-12376921 chr18:12376870-12376882 chr18:12376911-12376920
34	JUND	chr18:12377543-12377852	HepG2	liver:	n/a	chr18:12377742-12377750 chr18:12377740-12377752 chr18:12377740-12377751 chr18:12377742-12377750 chr18:12377743-12377750 chr18:12377741-12377751
35	POLR2A	chr18:12377451-12377974	GM12878	blood:	n/a	n/a
36	ARID3A	chr18:12377631-12377955	HepG2	liver:	n/a	n/a
37	CTCF	chr18:12377640-12377790	GM12867	blood:	n/a	n/a
38	ELF1	chr18:12376661-12377885	K562	blood:	n/a	chr18:12376910-12376921 chr18:12376870-12376882 chr18:12376911-12376920
39	MAX	chr18:12376020-12377995	K562	blood:	n/a	chr18:12376873-12376883 chr18:12377741-12377750
40	SP1	chr18:12377028-12378002	A549	lung:	n/a	chr18:12377520-12377531 chr18:12377483-12377494 chr18:12377249-12377258 chr18:12377250-12377259 chr18:12377248-12377260 chr18:12377248-12377260 chr18:12377249-12377258
41	ESRRA	chr18:12376420-12377939	HepG2	liver:	n/a	chr18:12377087-12377100 chr18:12376883-12376899 chr18:12376694-12376704 chr18:12376887-12376899 chr18:12376684-12376702 chr18:12376694-12376704 chr18:12376887-12376897 chr18:12376681-12376700 chr18:12376690-12376706 chr18:12376887-12376897 chr18:12376886-12376899
42	FOS	chr18:12377623-12377861	MCF10A-Er-Src	breast:	n/a	chr18:12377742-12377750 chr18:12377740-12377752 chr18:12377742-12377750 chr18:12377743-12377750 chr18:12377740-12377751 chr18:12377741-12377751
43	CTCF	chr18:12377680-12377830	HCT-116	colon:	n/a	n/a
44	CTCF	chr18:12377682-12377810	GM12892	blood:	n/a	n/a
45	FOSL2	chr18:12377513-12378057	A549	lung:	n/a	chr18:12377742-12377750 chr18:12377740-12377752 chr18:12377742-12377750 chr18:12377743-12377750 chr18:12377741-12377751
46	PBX3	chr18:12376922-12377973	SK-N-SH	brain:	n/a	n/a
47	FOS	chr18:12377580-12377776	MCF10A-Er-Src	breast:	n/a	chr18:12377742-12377750 chr18:12377740-12377752 chr18:12377742-12377750 chr18:12377743-12377750 chr18:12377740-12377751 chr18:12377741-12377751
48	POLR2A	chr18:12376628-12377867	GM10847	blood:	n/a	n/a
49	SP1	chr18:12376980-12378063	H1-hESC	embryonic stem cell:	n/a	chr18:12377520-12377531 chr18:12377483-12377494 chr18:12377249-12377258 chr18:12377250-12377259 chr18:12377248-12377260 chr18:12377248-12377260 chr18:12377249-12377258
50	MXI1	chr18:12375485-12378532	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12377168..12379207-chr18:12397711..12400933,3	K562	blood:
2	chr18:12377233..12378156-chr5:1523978..1524861,2	HCT-116	colon:
3	chr18:12306891..12312604-chr18:12376208..12378768,5	K562	blood:
4	chr18:12375314..12379217-chr18:12700733..12704866,11	K562	blood:
5	chr18:12376943..12379295-chr18:12946308..12947818,2	K562	blood:
6	chr18:12358323..12362507-chr18:12375018..12379122,7	K562	blood:
7	chr18:12375743..12378274-chr18:12418543..12422031,3	MCF-7	breast:
8	chr18:12375996..12378292-chr18:12406153..12409059,2	MCF-7	breast:
9	chr18:12306558..12308875-chr18:12376128..12379112,4	MCF-7	breast:
10	chr18:12374049..12378632-chr18:12655494..12660049,8	K562	blood:
11	chr18:12374593..12378692-chr18:12406477..12410976,5	K562	blood:
12	chr18:12375261..12378325-chr18:12405563..12409497,4	MCF-7	breast:
13	chr18:12377344..12378039-chr19:39832083..39833055,2	MCF-7	breast:
14	chr18:12375798..12379149-chr18:12946624..12949226,4	MCF-7	breast:
15	chr18:12375564..12378929-chr18:12655169..12659722,7	MCF-7	breast:
16	chr18:12376063..12377849-chr18:12702588..12704602,2	MCF-7	breast:
17	chr18:12372972..12377735-chr18:12656683..12660675,6	K562	blood:
18	chr18:12375835..12378198-chr18:12677932..12680535,3	K562	blood:
19	chr18:12376849..12377806-chr9:86594670..86595620,2	Hela-S3	cervix:
20	chr18:12305251..12310573-chr18:12373540..12378768,12	K562	blood:
21	chr18:12373949..12378992-chr18:12946352..12949410,8	K562	blood:
22	chr18:12307869..12309956-chr18:12375801..12377728,3	MCF-7	breast:
23	chr18:12376694..12378343-chr18:12532136..12534106,2	MCF-7	breast:
24	chr18:11979615..11982143-chr18:12376173..12378788,2	K562	blood:
25	chr18:12375309..12380137-chr18:12701387..12704274,11	K562	blood:
26	chr18:12375636..12378066-chr18:12991064..12992748,2	K562	blood:
27	chr16:771026..772819-chr18:12375664..12378170,2	MCF-7	breast:

Variant related genes	Relation type
AFG3L2	TF binding region
ENSG00000141385	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000141401	Chromatin interaction
ENSG00000176014	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000141391	Chromatin interaction
ENSG00000103254	Chromatin interaction
ENSG00000251937	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000238309	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000153395	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11659246	0.80[ASN][1000 genomes]
rs11660106	0.80[ASN][1000 genomes]
rs11661684	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11661708	0.95[ASN][1000 genomes]
rs11663340	0.80[ASN][1000 genomes]
rs11664255	0.80[ASN][1000 genomes]
rs11664282	0.80[ASN][1000 genomes]
rs11872615	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12327346	0.96[ASN][1000 genomes]
rs28470464	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28823942	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3819091	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6416994	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231304	0.85[ASN][1000 genomes]
rs7233290	0.85[ASN][1000 genomes]
rs7235929	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237135	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72875309	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7504616	0.80[ASN][1000 genomes]
rs9944742	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9946108	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9950665	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9964041	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9964437	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9966470	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv1060728	chr18:12364077-12410409	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 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	chr18:12375000-12378000	Active TSS	HSMM	muscle
2	chr18:12375200-12378200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr18:12375200-12378400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr18:12375200-12378400	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr18:12375200-12378400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr18:12375400-12377800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr18:12375400-12378200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr18:12375400-12378400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr18:12375400-12378400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr18:12375400-12378600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:12375600-12377800	Active TSS	Muscle Satellite Cultured Cells	--
12	chr18:12375600-12378000	Active TSS	Hela-S3	cervix
13	chr18:12375600-12378200	Active TSS	Left Ventricle	heart
14	chr18:12375600-12378200	Active TSS	A549	lung
15	chr18:12375600-12378400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr18:12375600-12378600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr18:12375800-12377800	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr18:12375800-12378000	Active TSS	Gastric	stomach
19	chr18:12375800-12378400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr18:12375800-12378600	Active TSS	HMEC	breast
21	chr18:12376000-12377800	Active TSS	GM12878-XiMat	blood
22	chr18:12376000-12378400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr18:12376000-12378400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr18:12376000-12378400	Active TSS	Fetal Kidney	kidney
25	chr18:12376000-12378400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr18:12376200-12378000	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr18:12376200-12378200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr18:12376200-12378200	Active TSS	Fetal Intestine Large	intestine
29	chr18:12376200-12378200	Active TSS	Ovary	ovary
30	chr18:12376200-12378400	Bivalent/Poised TSS	HepG2	liver
31	chr18:12376200-12378400	Active TSS	HSMMtube	muscle
32	chr18:12376400-12377800	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr18:12376400-12377800	Active TSS	Brain Anterior Caudate	brain
34	chr18:12376400-12377800	Active TSS	Brain Hippocampus Middle	brain
35	chr18:12376400-12377800	Active TSS	Fetal Stomach	stomach
36	chr18:12376400-12377800	Active TSS	Lung	lung
37	chr18:12376400-12377800	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr18:12376400-12377800	Active TSS	Rectal Smooth Muscle	rectum
39	chr18:12376400-12377800	Active TSS	Stomach Mucosa	stomach
40	chr18:12376400-12377800	Active TSS	Osteobl	bone
41	chr18:12376400-12378000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr18:12376400-12378000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr18:12376400-12378000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr18:12376400-12378000	Active TSS	Small Intestine	intestine
45	chr18:12376400-12378000	Active TSS	NHEK	skin
46	chr18:12376400-12378200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr18:12376400-12378200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr18:12376400-12378200	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr18:12376400-12378200	Active TSS	Aorta	Aorta
50	chr18:12376400-12378200	Active TSS	Brain Angular Gyrus	brain

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