Variant report

Variant	rs9964437
Chromosome Location	chr18:12377549-12377550
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	POLR2A	chr18:12377523-12377919	SK-N-MC	brain:	n/a	n/a
2	EGR1	chr18:12377177-12377666	K562	blood:	n/a	n/a
3	USF1	chr18:12377288-12377646	GM12878	blood:	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	MYC	chr18:12376126-12377946	K562	blood:	n/a	chr18:12376873-12376883 chr18:12377741-12377750
9	TEAD4	chr18:12377368-12378058	ECC-1	luminal epithelium:	n/a	chr18:12377784-12377793
10	CREB1	chr18:12376642-12377829	A549	lung:	n/a	n/a
11	SIN3AK20	chr18:12376391-12377931	K562	blood:	n/a	n/a
12	BHLHE40	chr18:12376078-12378109	K562	blood:	n/a	chr18:12377229-12377245 chr18:12377654-12377670 chr18:12376281-12376302
13	USF1	chr18:12377295-12377764	A549	lung:	n/a	chr18:12377654-12377670
14	MXI1	chr18:12376052-12377970	Hela-S3	cervix:	n/a	n/a
15	MAX	chr18:12376261-12377907	K562	blood:	n/a	chr18:12376873-12376883 chr18:12377741-12377750
16	BHLHE40	chr18:12377243-12377761	HepG2	liver:	n/a	chr18:12377654-12377670
17	ZNF143	chr18:12377110-12377933	H1-hESC	embryonic stem cell:	n/a	n/a
18	ELF1	chr18:12376438-12378069	GM12878	blood:	n/a	chr18:12376910-12376921 chr18:12376870-12376882 chr18:12376911-12376920
19	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
20	POLR2A	chr18:12377451-12377974	GM12878	blood:	n/a	n/a
21	ELF1	chr18:12376661-12377885	K562	blood:	n/a	chr18:12376910-12376921 chr18:12376870-12376882 chr18:12376911-12376920
22	MAX	chr18:12376020-12377995	K562	blood:	n/a	chr18:12376873-12376883 chr18:12377741-12377750
23	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
24	BHLHE40	chr18:12377212-12377698	A549	lung:	n/a	chr18:12377229-12377245 chr18:12377654-12377670
25	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
26	FOSL2	chr18:12377513-12378057	A549	lung:	n/a	chr18:12377742-12377750 chr18:12377740-12377752 chr18:12377742-12377750 chr18:12377743-12377750 chr18:12377741-12377751
27	PBX3	chr18:12376922-12377973	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr18:12376628-12377867	GM10847	blood:	n/a	n/a
29	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
30	MXI1	chr18:12375485-12378532	SK-N-SH	brain:	n/a	n/a
31	MYC	chr18:12377449-12377557	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr18:12377509-12378012	A549	lung:	n/a	n/a
33	JUN	chr18:12375031-12378398	K562	blood:	n/a	chr18:12377742-12377750 chr18:12377740-12377752 chr18:12376614-12376626 chr18:12377742-12377750 chr18:12377743-12377750 chr18:12377741-12377751
34	RELA	chr18:12376350-12378084	GM19099	blood:	n/a	n/a
35	USF2	chr18:12376653-12377846	GM12878	blood:	n/a	chr18:12377229-12377245 chr18:12377654-12377670
36	MAX	chr18:12376141-12377952	HepG2	liver:	n/a	chr18:12376873-12376883 chr18:12377741-12377750
37	MAX	chr18:12376278-12377864	A549	lung:	n/a	chr18:12376873-12376883 chr18:12377741-12377750
38	POLR2A	chr18:12376524-12378166	PFSK-1	brain:	n/a	n/a
39	USF1	chr18:12377189-12378057	ECC-1	luminal epithelium:	n/a	chr18:12377229-12377245 chr18:12377654-12377670
40	MTA3	chr18:12377511-12378167	GM12878	blood:	n/a	n/a
41	MXI1	chr18:12376129-12378082	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr18:12376090-12378068	GM12891	blood:	n/a	n/a
43	USF1	chr18:12377219-12377808	SK-N-SH_RA	brain:	n/a	chr18:12377229-12377245 chr18:12377654-12377670
44	MXI1	chr18:12375851-12378340	IMR90	lung:	n/a	n/a
45	ELF1	chr18:12376650-12377981	K562	blood:	n/a	chr18:12376910-12376921 chr18:12376870-12376882 chr18:12376911-12376920
46	HMGN3	chr18:12376648-12377912	K562	blood:	n/a	chr18:12377743-12377752
47	TAF1	chr18:12376933-12377929	MCF-7	breast:	n/a	n/a
48	SIN3AK20	chr18:12377046-12377872	PFSK-1	brain:	n/a	n/a
49	FOSL2	chr18:12376603-12377978	HepG2	liver:	n/a	chr18:12377742-12377750 chr18:12377740-12377752 chr18:12376614-12376626 chr18:12377742-12377750 chr18:12377743-12377750 chr18:12377741-12377751
50	USF1	chr18:12377117-12377942	ECC-1	luminal epithelium:	n/a	chr18:12377229-12377245 chr18:12377654-12377670

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	chr18:12376835..12377579-chr20:44563110..44563749,2	Hela-S3	cervix:
8	chr18:12375743..12378274-chr18:12418543..12422031,3	MCF-7	breast:
9	chr18:12375996..12378292-chr18:12406153..12409059,2	MCF-7	breast:
10	chr18:12306558..12308875-chr18:12376128..12379112,4	MCF-7	breast:
11	chr18:12374049..12378632-chr18:12655494..12660049,8	K562	blood:
12	chr18:12374593..12378692-chr18:12406477..12410976,5	K562	blood:
13	chr18:12375261..12378325-chr18:12405563..12409497,4	MCF-7	breast:
14	chr18:12377344..12378039-chr19:39832083..39833055,2	MCF-7	breast:
15	chr18:12375798..12379149-chr18:12946624..12949226,4	MCF-7	breast:
16	chr18:12375564..12378929-chr18:12655169..12659722,7	MCF-7	breast:
17	chr18:12376063..12377849-chr18:12702588..12704602,2	MCF-7	breast:
18	chr18:12372972..12377735-chr18:12656683..12660675,6	K562	blood:
19	chr18:12375835..12378198-chr18:12677932..12680535,3	K562	blood:
20	chr18:12376849..12377806-chr9:86594670..86595620,2	Hela-S3	cervix:
21	chr18:12305251..12310573-chr18:12373540..12378768,12	K562	blood:
22	chr18:12373949..12378992-chr18:12946352..12949410,8	K562	blood:
23	chr18:12307869..12309956-chr18:12375801..12377728,3	MCF-7	breast:
24	chr18:12376694..12378343-chr18:12532136..12534106,2	MCF-7	breast:
25	chr18:11979615..11982143-chr18:12376173..12378788,2	K562	blood:
26	chr18:12375309..12380137-chr18:12701387..12704274,11	K562	blood:
27	chr18:12375636..12378066-chr18:12991064..12992748,2	K562	blood:
28	chr18:12376921..12377615-chr5:133340047..133340644,2	Hela-S3	cervix:
29	chr16:771026..772819-chr18:12375664..12378170,2	MCF-7	breast:

Variant related genes	Relation type
AFG3L2	TF binding region
ENSG00000266969	Chromatin interaction
ENSG00000100982	Chromatin interaction
ENSG00000141401	Chromatin interaction
ENSG00000141391	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000213585	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000238309	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000251937	Chromatin interaction
ENSG00000103254	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000176014	Chromatin interaction
ENSG00000153395	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000130755	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	0.97[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	0.98[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	0.98[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]
rs9964720	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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