Variant report

Variant	rs12956961
Chromosome Location	chr18:7945974-7945975
allele	G/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	JUND	chr18:7945871-7946307	SK-N-SH	brain:	n/a	chr18:7946039-7946050 chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
2	PBX3	chr18:7945888-7946257	SK-N-SH	brain:	n/a	n/a
3	EP300	chr18:7945579-7947037	A549	lung:	n/a	chr18:7946041-7946050 chr18:7946124-7946133
4	RAD21	chr18:7945828-7946301	A549	lung:	n/a	n/a
5	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
6	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
7	CEBPB	chr18:7945854-7946385	A549	lung:	n/a	chr18:7946277-7946289
8	USF2	chr18:7945920-7946212	Hela-S3	cervix:	n/a	n/a
9	FOSL2	chr18:7945788-7946299	SK-N-SH	brain:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
10	STAT3	chr18:7945942-7946474	MCF10A-Er-Src	breast:	n/a	n/a
11	SP1	chr18:7945621-7947120	A549	lung:	n/a	chr18:7946544-7946554
12	USF1	chr18:7945858-7946134	A549	lung:	n/a	n/a
13	JUND	chr18:7945941-7946220	HepG2	liver:	n/a	chr18:7946039-7946050 chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
14	FOSL2	chr18:7945796-7946344	MCF-7	breast:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
15	NR3C1	chr18:7945861-7946249	A549	lung:	n/a	n/a
16	STAT3	chr18:7945941-7946240	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr18:7945897-7946176	GM12878	blood:	n/a	chr18:7946041-7946050 chr18:7946124-7946133
18	FOXA2	chr18:7945905-7946296	A549	lung:	n/a	chr18:7946077-7946089
19	POLR2A	chr18:7945752-7947093	MCF10A-Er-Src	breast:	n/a	n/a
20	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
21	NR3C1	chr18:7945879-7946240	A549	lung:	n/a	n/a
22	NR3C1	chr18:7945813-7946261	A549	lung:	n/a	n/a
23	TCF12	chr18:7945786-7946326	SK-N-SH	brain:	n/a	n/a
24	GATA3	chr18:7945615-7947178	A549	lung:	n/a	chr18:7946126-7946135 chr18:7946123-7946132 chr18:7945973-7945980
25	CHD2	chr18:7945882-7946267	Hela-S3	cervix:	n/a	n/a
26	JUND	chr18:7945908-7946326	A549	lung:	n/a	chr18:7946039-7946050 chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
27	NR3C1	chr18:7945836-7946181	A549	lung:	n/a	n/a
28	FOSL2	chr18:7945808-7946323	A549	lung:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
29	CEBPB	chr18:7945827-7947031	Hela-S3	cervix:	n/a	chr18:7946277-7946289
30	POLR2A	chr18:7945877-7946284	U87	brain:	n/a	n/a
31	FOSL1	chr18:7945700-7946293	HCT-116	colon:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
32	MYC	chr18:7945943-7946250	MCF10A-Er-Src	breast:	n/a	n/a
33	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
34	JUND	chr18:7945833-7946333	Hela-S3	cervix:	n/a	chr18:7946039-7946050 chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
35	CEBPB	chr18:7945831-7946589	A549	lung:	n/a	chr18:7946277-7946289
36	TBP	chr18:7945874-7946067	GM12878	blood:	n/a	n/a
37	TCF12	chr18:7945867-7946192	A549	lung:	n/a	n/a
38	MAX	chr18:7945794-7946374	A549	lung:	n/a	n/a
39	TBP	chr18:7945931-7946364	Hela-S3	cervix:	n/a	n/a
40	STAT3	chr18:7945941-7946249	MCF10A-Er-Src	breast:	n/a	n/a
41	STAT3	chr18:7945837-7946229	Hela-S3	cervix:	n/a	n/a
42	FOSL2	chr18:7945572-7947091	A549	lung:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
43	BCL3	chr18:7945716-7946372	A549	lung:	n/a	n/a
44	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
45	CHD2	chr18:7945949-7946146	GM12878	blood:	n/a	n/a
46	MYC	chr18:7945884-7946313	MCF10A-Er-Src	breast:	n/a	n/a
47	E2F4	chr18:7945959-7946241	MCF10A-Er-Src	breast:	n/a	n/a
48	REST	chr18:7945694-7946575	A549	lung:	n/a	n/a
49	JUN	chr18:7945815-7946402	Hela-S3	cervix:	n/a	chr18:7946121-7946132 chr18:7946126-7946133 chr18:7946124-7946133 chr18:7946041-7946050 chr18:7946041-7946048
50	EP300	chr18:7945928-7946176	GM12878	blood:	n/a	chr18:7946041-7946050 chr18:7946124-7946133

Variant related genes	Relation type
PTPRM	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10153443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs12326176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12326185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs12954431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs12957388	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs12957993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959314	0.90[EUR][1000 genomes]
rs12960276	0.90[EUR][1000 genomes]
rs12963759	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12966777	0.90[EUR][1000 genomes]
rs12968232	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13381485	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16952586	1.00[CHB][hapmap]
rs16952705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs16952722	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs28434244	0.91[EUR][1000 genomes]
rs34017251	0.91[EUR][1000 genomes]
rs34046553	0.91[EUR][1000 genomes]
rs34049036	0.91[EUR][1000 genomes]
rs34296167	0.91[EUR][1000 genomes]
rs34554615	0.90[EUR][1000 genomes]
rs34580701	0.91[EUR][1000 genomes]
rs35308699	0.91[EUR][1000 genomes]
rs35434291	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35521625	0.90[EUR][1000 genomes]
rs35558945	0.90[EUR][1000 genomes]
rs35822807	0.90[EUR][1000 genomes]
rs35830277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36093720	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7239786	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7240582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8087770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8087884	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs8089133	0.91[EUR][1000 genomes]
rs8092781	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9807495	0.86[EUR][1000 genomes]
rs9952741	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs9956981	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9961079	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs9966320	1.00[CHB][hapmap]

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:70 , 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	chr18:7932000-7946000	Weak transcription	Brain Anterior Caudate	brain
4	chr18:7932200-7961000	Weak transcription	HepG2	liver
5	chr18:7937600-7947000	Weak transcription	Thymus	Thymus
6	chr18:7937600-7949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr18:7937600-7955200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr18:7938000-7946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr18:7941000-7946600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr18:7941400-7955000	Weak transcription	Psoas Muscle	Psoas
11	chr18:7941800-7946000	Weak transcription	Brain Substantia Nigra	brain
12	chr18:7941800-7946800	Weak transcription	Lung	lung
13	chr18:7941800-7966400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr18:7942000-7946400	Weak transcription	Right Atrium	heart
15	chr18:7942000-7946600	Weak transcription	Fetal Heart	heart
16	chr18:7942000-7946800	Weak transcription	Brain Angular Gyrus	brain
17	chr18:7942000-7955200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr18:7942000-7955200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr18:7942200-7946000	Weak transcription	Pancreas	Pancrea
20	chr18:7942200-7955200	Weak transcription	Fetal Muscle Leg	muscle
21	chr18:7942600-7946800	Weak transcription	Gastric	stomach
22	chr18:7943000-7946600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr18:7943000-7946800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr18:7944200-7946600	Enhancers	Hela-S3	cervix
25	chr18:7944200-7946800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr18:7944600-7946200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr18:7945200-7946200	Enhancers	NHDF-Ad	bronchial
28	chr18:7945200-7946600	Enhancers	Ovary	ovary
29	chr18:7945200-7946800	Enhancers	Rectal Smooth Muscle	rectum
30	chr18:7945400-7946200	Enhancers	Aorta	Aorta
31	chr18:7945400-7946200	Enhancers	Osteobl	bone
32	chr18:7945400-7946400	Enhancers	Fetal Intestine Large	intestine
33	chr18:7945400-7946600	Enhancers	HMEC	breast
34	chr18:7945400-7946800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr18:7945400-7946800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr18:7945400-7946800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr18:7945400-7948000	Enhancers	Small Intestine	intestine
38	chr18:7945600-7946000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr18:7945600-7946200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr18:7945600-7946400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr18:7945600-7946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr18:7945600-7946400	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr18:7945600-7946400	Enhancers	NHLF	lung
44	chr18:7945600-7946600	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr18:7945600-7946600	Enhancers	Duodenum Mucosa	Duodenum
46	chr18:7945600-7946600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr18:7945600-7946600	Enhancers	HSMMtube	muscle
48	chr18:7945600-7946800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr18:7945600-7946800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr18:7945600-7946800	Enhancers	Brain Germinal Matrix	brain

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