Variant report

Variant	rs9962120
Chromosome Location	chr18:7946698-7946699
allele	C/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	EP300	chr18:7945579-7947037	A549	lung:	n/a	chr18:7946041-7946050 chr18:7946124-7946133
2	MYC	chr18:7946676-7947049	MCF10A-Er-Src	breast:	n/a	n/a
3	GABPA	chr18:7946585-7947044	A549	lung:	n/a	n/a
4	TAF1	chr18:7946632-7947087	H1-neurons	neurons:	n/a	n/a
5	GATA2	chr18:7946657-7947288	HUVEC	blood vessel:	n/a	n/a
6	RAD21	chr18:7946688-7947162	IMR90	lung:	n/a	n/a
7	GATA3	chr18:7946614-7947114	SK-N-SH	brain:	n/a	n/a
8	SP1	chr18:7945621-7947120	A549	lung:	n/a	chr18:7946544-7946554
9	CHD2	chr18:7946676-7947002	GM12878	blood:	n/a	n/a
10	MAX	chr18:7946696-7947123	Hela-S3	cervix:	n/a	n/a
11	MAX	chr18:7946610-7947226	A549	lung:	n/a	n/a
12	KAP1	chr18:7946556-7947022	U2OS	brain:	n/a	chr18:7946588-7946596
13	NR3C1	chr18:7946689-7947032	A549	lung:	n/a	n/a
14	CHD2	chr18:7946669-7947331	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr18:7945752-7947093	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr18:7946605-7947182	HCT-116	colon:	n/a	n/a
17	GABPA	chr18:7946624-7946990	A549	lung:	n/a	n/a
18	NR3C1	chr18:7946667-7947103	A549	lung:	n/a	n/a
19	POLR2A	chr18:7946564-7947149	U87	brain:	n/a	n/a
20	TBP	chr18:7946649-7947019	GM12878	blood:	n/a	n/a
21	GATA3	chr18:7945615-7947178	A549	lung:	n/a	chr18:7946126-7946135 chr18:7946123-7946132 chr18:7945973-7945980
22	CEBPB	chr18:7945827-7947031	Hela-S3	cervix:	n/a	chr18:7946277-7946289
23	TAF1	chr18:7946674-7947101	H1-neurons	neurons:	n/a	n/a
24	POLR2A	chr18:7946671-7947151	H1-neurons	neurons:	n/a	n/a
25	GATA3	chr18:7946523-7947110	SK-N-SH	brain:	n/a	n/a
26	RFX5	chr18:7946662-7947036	Hela-S3	cervix:	n/a	n/a
27	NR3C1	chr18:7946688-7947042	A549	lung:	n/a	n/a
28	GABPA	chr18:7946629-7946989	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr18:7946665-7947149	U87	brain:	n/a	n/a
30	POLR2A	chr18:7946558-7947296	U87	brain:	n/a	n/a
31	FOSL2	chr18:7945572-7947091	A549	lung:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
32	CEBPB	chr18:7946666-7947039	IMR90	lung:	n/a	n/a
33	SP1	chr18:7946601-7947088	A549	lung:	n/a	n/a
34	POLR2A	chr18:7946697-7947063	GM12878	blood:	n/a	n/a
35	GTF2F1	chr18:7946672-7947077	Hela-S3	cervix:	n/a	n/a
36	CEBPB	chr18:7946675-7947003	A549	lung:	n/a	n/a
37	MXI1	chr18:7946683-7946999	GM12878	blood:	n/a	n/a
38	GABPA	chr18:7946629-7947050	SK-N-SH	brain:	n/a	n/a
39	MAX	chr18:7946698-7947164	A549	lung:	n/a	n/a
40	TBP	chr18:7946636-7947089	Hela-S3	cervix:	n/a	n/a
41	YY1	chr18:7946673-7947041	SK-N-SH_RA	brain:	n/a	n/a
42	STAT3	chr18:7946689-7946959	MCF10A-Er-Src	breast:	n/a	n/a
43	GABPA	chr18:7946575-7947138	SK-N-SH	brain:	n/a	n/a
44	REST	chr18:7946455-7947417	H1-neurons	neurons:	n/a	n/a
45	EP300	chr18:7945820-7947036	Hela-S3	cervix:	n/a	chr18:7946041-7946050 chr18:7946124-7946133
46	ZNF143	chr18:7946691-7946938	GM12878	blood:	n/a	n/a
47	MXI1	chr18:7946538-7947322	Hela-S3	cervix:	n/a	n/a
48	TAF1	chr18:7946636-7947090	A549	lung:	n/a	n/a
49	POLR2A	chr18:7946558-7947229	U87	brain:	n/a	n/a
50	TCF12	chr18:7945551-7947134	A549	lung:	n/a	n/a

Variant related genes	Relation type
PTPRM	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10164001	0.88[AFR][1000 genomes]
rs13381990	0.83[AFR][1000 genomes]
rs28429357	0.80[AFR][1000 genomes]
rs28714420	0.80[AFR][1000 genomes]
rs7230073	0.86[AFR][1000 genomes]
rs7239466	0.85[AFR][1000 genomes]
rs9954126	0.81[AFR][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	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7932200-7961000	Weak transcription	HepG2	liver
2	chr18:7937600-7947000	Weak transcription	Thymus	Thymus
3	chr18:7937600-7949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:7937600-7955200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:7938000-7946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:7941400-7955000	Weak transcription	Psoas Muscle	Psoas
7	chr18:7941800-7946800	Weak transcription	Lung	lung
8	chr18:7941800-7966400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr18:7942000-7946800	Weak transcription	Brain Angular Gyrus	brain
10	chr18:7942000-7955200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr18:7942000-7955200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr18:7942200-7955200	Weak transcription	Fetal Muscle Leg	muscle
13	chr18:7942600-7946800	Weak transcription	Gastric	stomach
14	chr18:7943000-7946800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr18:7944200-7946800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr18:7945200-7946800	Enhancers	Rectal Smooth Muscle	rectum
17	chr18:7945400-7946800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr18:7945400-7946800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr18:7945400-7946800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr18:7945400-7948000	Enhancers	Small Intestine	intestine
21	chr18:7945600-7946800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr18:7945600-7946800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:7945600-7946800	Enhancers	Brain Germinal Matrix	brain
24	chr18:7945600-7946800	Enhancers	HSMM	muscle
25	chr18:7945600-7946800	Enhancers	NH-A	brain
26	chr18:7945600-7946800	Enhancers	NHEK	skin
27	chr18:7945600-7947200	Enhancers	Colon Smooth Muscle	Colon
28	chr18:7945600-7947200	Enhancers	Fetal Stomach	stomach
29	chr18:7945600-7947800	Enhancers	HUVEC	blood vessel
30	chr18:7945600-7950400	Weak transcription	Left Ventricle	heart
31	chr18:7945800-7946800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr18:7945800-7946800	Enhancers	Adipose Nuclei	Adipose
33	chr18:7945800-7946800	Enhancers	Fetal Lung	lung
34	chr18:7945800-7946800	Enhancers	Stomach Smooth Muscle	stomach
35	chr18:7945800-7947200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr18:7945800-7947200	Enhancers	Stomach Mucosa	stomach
37	chr18:7945800-7947800	Enhancers	Right Ventricle	heart
38	chr18:7946000-7946800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr18:7946000-7946800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr18:7946000-7947000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr18:7946000-7948000	Enhancers	Pancreas	Pancrea
42	chr18:7946200-7946800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr18:7946200-7946800	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr18:7946200-7946800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr18:7946200-7946800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr18:7946200-7947200	Flanking Active TSS	NHDF-Ad	bronchial
47	chr18:7946200-7947400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr18:7946200-7947400	Flanking Active TSS	Osteobl	bone
49	chr18:7946200-7947800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr18:7946200-7958200	Weak transcription	Aorta	Aorta

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