Variant report

Variant	rs9961079
Chromosome Location	chr18:7946334-7946335
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	EP300	chr18:7945579-7947037	A549	lung:	n/a	chr18:7946041-7946050 chr18:7946124-7946133
2	JUND	chr18:7945762-7946350	HCT-116	colon:	n/a	chr18:7946039-7946050 chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
3	GATA3	chr18:7946286-7946439	SH-SY5Y	brain:	n/a	n/a
4	FOS	chr18:7945652-7946500	MCF10A-Er-Src	breast:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048 chr18:7946123-7946134
5	CEBPB	chr18:7945854-7946385	A549	lung:	n/a	chr18:7946277-7946289
6	STAT3	chr18:7945942-7946474	MCF10A-Er-Src	breast:	n/a	n/a
7	SP1	chr18:7945621-7947120	A549	lung:	n/a	chr18:7946544-7946554
8	FOSL2	chr18:7945796-7946344	MCF-7	breast:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
9	POLR2A	chr18:7945752-7947093	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr18:7945794-7946426	HUVEC	blood vessel:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048 chr18:7946123-7946134
11	GATA3	chr18:7945615-7947178	A549	lung:	n/a	chr18:7946126-7946135 chr18:7946123-7946132 chr18:7945973-7945980
12	CEBPB	chr18:7945827-7947031	Hela-S3	cervix:	n/a	chr18:7946277-7946289
13	JUND	chr18:7945795-7946364	A549	lung:	n/a	chr18:7946039-7946050 chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
14	CEBPB	chr18:7945831-7946589	A549	lung:	n/a	chr18:7946277-7946289
15	MAX	chr18:7945794-7946374	A549	lung:	n/a	n/a
16	TBP	chr18:7945931-7946364	Hela-S3	cervix:	n/a	n/a
17	FOSL2	chr18:7945572-7947091	A549	lung:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
18	BCL3	chr18:7945716-7946372	A549	lung:	n/a	n/a
19	FOS	chr18:7945860-7946391	MCF10A-Er-Src	breast:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048 chr18:7946123-7946134
20	REST	chr18:7945694-7946575	A549	lung:	n/a	n/a
21	JUN	chr18:7945815-7946402	Hela-S3	cervix:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
22	SP1	chr18:7945687-7946483	A549	lung:	n/a	n/a
23	GATA3	chr18:7945857-7946463	A549	lung:	n/a	chr18:7946126-7946135 chr18:7946123-7946132 chr18:7945973-7945980
24	JUND	chr18:7945920-7946336	SK-N-SH	brain:	n/a	chr18:7946039-7946050 chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
25	MAX	chr18:7945719-7946446	A549	lung:	n/a	n/a
26	FOXA2	chr18:7945888-7946546	A549	lung:	n/a	chr18:7946077-7946089
27	RAD21	chr18:7945704-7946392	A549	lung:	n/a	n/a
28	EP300	chr18:7945820-7947036	Hela-S3	cervix:	n/a	chr18:7946041-7946050 chr18:7946124-7946133
29	TCF12	chr18:7945551-7947134	A549	lung:	n/a	n/a
30	EP300	chr18:7945654-7946651	A549	lung:	n/a	chr18:7946041-7946050 chr18:7946124-7946133

Variant related genes	Relation type
PTPRM	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10153443	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12326176	0.85[EUR][1000 genomes]
rs12326185	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12954431	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12956961	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs12957388	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12957993	0.86[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs12959314	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12960276	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12963759	0.90[EUR][1000 genomes]
rs12966777	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12968232	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13381485	0.85[EUR][1000 genomes]
rs16952705	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16952722	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28434244	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34017251	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34046553	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34049036	1.00[EUR][1000 genomes]
rs34296167	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34554615	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34580701	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35308699	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35434291	0.84[EUR][1000 genomes]
rs35521625	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35558945	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35822807	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35830277	0.87[EUR][1000 genomes]
rs36093720	0.85[EUR][1000 genomes]
rs7239786	0.83[ASW][hapmap];0.86[EUR][1000 genomes]
rs7240582	0.85[EUR][1000 genomes]
rs8087770	0.85[EUR][1000 genomes]
rs8087884	0.86[CEU][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8089133	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8092781	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807495	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9952741	0.80[CEU][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9956981	0.85[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9961079	NAPG	cis	parietal	SCAN
rs9961079	BOK	trans	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7927800-7946600	Weak transcription	Fetal Kidney	kidney
2	chr18:7928000-7946600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr18:7932200-7961000	Weak transcription	HepG2	liver
4	chr18:7937600-7947000	Weak transcription	Thymus	Thymus
5	chr18:7937600-7949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:7937600-7955200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr18:7938000-7946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:7941000-7946600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr18:7941400-7955000	Weak transcription	Psoas Muscle	Psoas
10	chr18:7941800-7946800	Weak transcription	Lung	lung
11	chr18:7941800-7966400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr18:7942000-7946400	Weak transcription	Right Atrium	heart
13	chr18:7942000-7946600	Weak transcription	Fetal Heart	heart
14	chr18:7942000-7946800	Weak transcription	Brain Angular Gyrus	brain
15	chr18:7942000-7955200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr18:7942000-7955200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr18:7942200-7955200	Weak transcription	Fetal Muscle Leg	muscle
18	chr18:7942600-7946800	Weak transcription	Gastric	stomach
19	chr18:7943000-7946600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr18:7943000-7946800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr18:7944200-7946600	Enhancers	Hela-S3	cervix
22	chr18:7944200-7946800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr18:7945200-7946600	Enhancers	Ovary	ovary
24	chr18:7945200-7946800	Enhancers	Rectal Smooth Muscle	rectum
25	chr18:7945400-7946400	Enhancers	Fetal Intestine Large	intestine
26	chr18:7945400-7946600	Enhancers	HMEC	breast
27	chr18:7945400-7946800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr18:7945400-7946800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr18:7945400-7946800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:7945400-7948000	Enhancers	Small Intestine	intestine
31	chr18:7945600-7946400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr18:7945600-7946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr18:7945600-7946400	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr18:7945600-7946400	Enhancers	NHLF	lung
35	chr18:7945600-7946600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr18:7945600-7946600	Enhancers	Duodenum Mucosa	Duodenum
37	chr18:7945600-7946600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr18:7945600-7946600	Enhancers	HSMMtube	muscle
39	chr18:7945600-7946800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr18:7945600-7946800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr18:7945600-7946800	Enhancers	Brain Germinal Matrix	brain
42	chr18:7945600-7946800	Enhancers	HSMM	muscle
43	chr18:7945600-7946800	Enhancers	NH-A	brain
44	chr18:7945600-7946800	Enhancers	NHEK	skin
45	chr18:7945600-7947200	Enhancers	Colon Smooth Muscle	Colon
46	chr18:7945600-7947200	Enhancers	Fetal Stomach	stomach
47	chr18:7945600-7947800	Enhancers	HUVEC	blood vessel
48	chr18:7945600-7950400	Weak transcription	Left Ventricle	heart
49	chr18:7945800-7946400	Active TSS	A549	lung
50	chr18:7945800-7946600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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