Variant report

Variant	rs2292758
Chromosome Location	chr18:12884466-12884467
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	chr18:12882099-12885668	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr18:12883299-12884614	A549	lung:	n/a	n/a
3	POLR2A	chr18:12883006-12884887	Raji	blood:	n/a	n/a
4	TBP	chr18:12883589-12884580	K562	blood:	n/a	n/a
5	POLR2A	chr18:12883379-12884765	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr18:12883095-12884708	MCF-7	breast:	n/a	n/a
7	POLR2A	chr18:12882820-12884672	GM18505	blood:	n/a	n/a
8	MYC	chr18:12883225-12884659	K562	blood:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
9	POLR2A	chr18:12883564-12884640	HCT-116	colon:	n/a	n/a
10	POLR2A	chr18:12883333-12884555	PFSK-1	brain:	n/a	n/a
11	ELK1	chr18:12883645-12884893	GM12878	blood:	n/a	n/a
12	EBF1	chr18:12884416-12884678	GM12878	blood:	n/a	chr18:12884550-12884560
13	MYC	chr18:12883417-12884786	MCF10A-Er-Src	breast:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
14	MXI1	chr18:12882814-12886050	GM12878	blood:	n/a	n/a
15	MYC	chr18:12883034-12884687	NB4	blood:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
16	MAX	chr18:12882960-12884616	K562	blood:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
17	TCF3	chr18:12884347-12884622	GM12878	blood:	n/a	n/a
18	NRF1	chr18:12883290-12884928	SK-N-SH	brain:	n/a	chr18:12884252-12884261 chr18:12884152-12884163 chr18:12883915-12883926 chr18:12883830-12883841 chr18:12883912-12883926 chr18:12883529-12883543 chr18:12884225-12884239 chr18:12883827-12883841 chr18:12884228-12884239 chr18:12884228-12884242 chr18:12884228-12884237 chr18:12884167-12884178 chr18:12884228-12884239 chr18:12884230-12884239
19	MAX	chr18:12883572-12884702	H1-hESC	embryonic stem cell:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
20	POLR2A	chr18:12882559-12886033	GM12891	blood:	n/a	n/a
21	CREB1	chr18:12883501-12884646	GM12878	blood:	n/a	n/a
22	MAX	chr18:12883426-12884774	ECC-1	luminal epithelium:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
23	SIN3AK20	chr18:12883470-12884499	MCF-7	breast:	n/a	n/a
24	EP300	chr18:12883645-12884854	GM12878	blood:	n/a	chr18:12884142-12884158
25	POLR2A	chr18:12883446-12884569	Gliobla	brain:	n/a	n/a
26	POLR2A	chr18:12883564-12884650	GM10847	blood:	n/a	n/a
27	POLR2A	chr18:12883169-12884507	HL-60	blood:	n/a	n/a
28	CREB1	chr18:12883236-12884730	HepG2	liver:	n/a	n/a
29	POLR2A	chr18:12883587-12884596	HCT-116	colon:	n/a	n/a
30	TCF12	chr18:12884375-12884784	GM12878	blood:	n/a	n/a
31	POLR2A	chr18:12883058-12884733	GM19193	blood:	n/a	n/a
32	TAF1	chr18:12883433-12884796	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr18:12882859-12886028	GM12878	blood:	n/a	n/a
34	POLR2A	chr18:12883274-12884626	ECC-1	luminal epithelium:	n/a	n/a
35	E2F4	chr18:12883551-12884605	K562	blood:	n/a	chr18:12884229-12884238 chr18:12883989-12884001 chr18:12883940-12883949 chr18:12883916-12883925 chr18:12884252-12884261 chr18:12883831-12883840
36	YY1	chr18:12883218-12884490	HepG2	liver:	n/a	chr18:12883935-12883949 chr18:12883940-12883949 chr18:12884252-12884261 chr18:12883398-12883412 chr18:12883909-12883923
37	POLR2A	chr18:12883560-12884614	HepG2	liver:	n/a	n/a
38	CCNT2	chr18:12883289-12884604	K562	blood:	n/a	chr18:12884252-12884261
39	EP300	chr18:12883393-12884725	GM12878	blood:	n/a	chr18:12884142-12884158
40	USF2	chr18:12884423-12884721	GM12878	blood:	n/a	n/a
41	SPI1	chr18:12884391-12884866	GM12878	blood:	n/a	n/a
42	POLR2A	chr18:12883277-12884851	H1-hESC	embryonic stem cell:	n/a	n/a
43	MYC	chr18:12882688-12884769	K562	blood:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
44	TAF1	chr18:12884386-12884630	H1-hESC	embryonic stem cell:	n/a	n/a
45	SMARCB1	chr18:12882991-12884671	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr18:12884378-12886072	GM12878	blood:	n/a	n/a
47	HCFC1	chr18:12883431-12884572	K562	blood:	n/a	n/a
48	MAX	chr18:12883550-12884646	SK-N-SH	brain:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
49	MAX	chr18:12883584-12884522	HepG2	liver:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
50	HA-E2F1	chr18:12883419-12884541	Hela-S3	cervix:	n/a	chr18:12884229-12884238 chr18:12883989-12884001 chr18:12883536-12883546 chr18:12883940-12883949 chr18:12883916-12883925 chr18:12884252-12884261 chr18:12883831-12883840

No.	Distal block	Cell Line	Cell type
1	chr15:65596946..65598700-chr18:12882626..12885488,2	MCF-7	breast:
2	chr11:75110573..75111082-chr18:12883776..12884593,2	Hela-S3	cervix:
3	chr18:12774117..12776643-chr18:12883699..12885836,3	K562	blood:
4	chr18:12880282..12885478-chr18:12946145..12950206,8	K562	blood:
5	chr18:12883825..12884548-chr19:56116434..56117103,2	Hela-S3	cervix:
6	chr1:28907896..28908672-chr18:12883704..12884487,2	Hela-S3	cervix:
7	chr18:12882771..12885367-chr18:12946819..12949664,2	MCF-7	breast:
8	chr16:69796121..69796656-chr18:12883876..12884654,2	Hela-S3	cervix:
9	chr11:59436284..59437132-chr18:12883857..12884750,2	Hela-S3	cervix:
10	chr18:12760116..12762309-chr18:12883836..12885442,2	K562	blood:
11	chr18:12883912..12884619-chr3:141205723..141206246,2	Hela-S3	cervix:
12	chr1:115212841..115213576-chr18:12883945..12884614,2	Hela-S3	cervix:
13	chr17:40272993..40273808-chr18:12884016..12884888,2	Hela-S3	cervix:
14	chr1:145382262..145383113-chr18:12883770..12884685,2	Hela-S3	cervix:
15	chr12:105501007..105501649-chr18:12884012..12884801,2	Hela-S3	cervix:
16	chr1:147806040..147807089-chr18:12883758..12884527,3	Hela-S3	cervix:
17	chr10:101190701..101191272-chr18:12884017..12884694,2	Hela-S3	cervix:
18	chr16:4475407..4476017-chr18:12883945..12884638,2	Hela-S3	cervix:

Variant related genes	Relation type
PTPN2	TF binding region
ENSG00000262246	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000108773	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000166889	Chromatin interaction
ENSG00000103423	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000198373	Chromatin interaction
ENSG00000224934	Chromatin interaction
ENSG00000197989	Chromatin interaction
ENSG00000260302	Chromatin interaction
ENSG00000155903	Chromatin interaction
ENSG00000201466	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000175984	Chromatin interaction
ENSG00000202408	Chromatin interaction
ENSG00000255355	Chromatin interaction
ENSG00000149273	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs2032174	0.86[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap]
rs2847288	0.95[CHD][hapmap];0.89[JPT][hapmap]
rs3826556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs45579734	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs471401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4797708	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs507304	0.83[ASN][1000 genomes]
rs513185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56384328	0.83[ASN][1000 genomes]
rs578377	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs58200120	0.83[ASN][1000 genomes]
rs59471125	0.83[ASN][1000 genomes]
rs607906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs60803113	0.83[ASN][1000 genomes]
rs622717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs637643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6505769	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs669822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs670671	0.83[ASN][1000 genomes]
rs683468	0.83[ASN][1000 genomes]
rs7238238	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7241650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72872144	0.82[ASN][1000 genomes]
rs73950681	0.81[ASN][1000 genomes]
rs73950683	0.83[ASN][1000 genomes]
rs73950684	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73950685	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8084365	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8091305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8098730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9954778	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9959061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs9961827	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9961931	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9966378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
6	nsv909407	chr18:12877060-12917703	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	n/a
7	esv3433183	chr18:12883052-12885400	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12882200-12885000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr18:12882200-12885000	Active TSS	A549	lung
3	chr18:12882200-12885000	Active TSS	HMEC	breast
4	chr18:12882200-12885000	Active TSS	NHLF	lung
5	chr18:12882400-12884600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr18:12882400-12884600	Active TSS	Fetal Thymus	thymus
7	chr18:12882400-12885000	Active TSS	GM12878-XiMat	blood
8	chr18:12882400-12885200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr18:12882400-12885600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr18:12882600-12884600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr18:12882600-12884600	Active TSS	Muscle Satellite Cultured Cells	--
12	chr18:12882600-12884600	Active TSS	Fetal Muscle Leg	muscle
13	chr18:12882600-12884600	Active TSS	Thymus	Thymus
14	chr18:12882600-12884600	Active TSS	HSMM	muscle
15	chr18:12882600-12884800	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr18:12882600-12884800	Active TSS	Psoas Muscle	Psoas
17	chr18:12882600-12885000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:12882600-12885000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr18:12882600-12885000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr18:12882600-12885000	Active TSS	Fetal Stomach	stomach
21	chr18:12882600-12885000	Active TSS	NHDF-Ad	bronchial
22	chr18:12882800-12884600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr18:12882800-12884600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr18:12882800-12884600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr18:12882800-12884800	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr18:12882800-12884800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr18:12882800-12884800	Active TSS	Stomach Mucosa	stomach
28	chr18:12882800-12885000	Active TSS	H9 Cell Line	embryonic stem cell
29	chr18:12882800-12885000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr18:12882800-12885000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr18:12882800-12885000	Active TSS	Fetal Intestine Small	intestine
32	chr18:12882800-12885000	Active TSS	Placenta	Placenta
33	chr18:12882800-12885200	Active TSS	Colonic Mucosa	Colon
34	chr18:12883000-12884600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr18:12883000-12884600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr18:12883000-12884600	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr18:12883000-12884600	Active TSS	Primary T cells from cord blood	blood
38	chr18:12883000-12884600	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr18:12883000-12884800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr18:12883000-12884800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:12883000-12884800	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr18:12883000-12884800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr18:12883000-12884800	Active TSS	Colon Smooth Muscle	Colon
44	chr18:12883000-12884800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr18:12883000-12884800	Active TSS	Esophagus	oesophagus
46	chr18:12883000-12884800	Active TSS	Fetal Kidney	kidney
47	chr18:12883000-12884800	Active TSS	Gastric	stomach
48	chr18:12883000-12884800	Active TSS	Ovary	ovary
49	chr18:12883000-12884800	Active TSS	Pancreas	Pancrea
50	chr18:12883000-12884800	Active TSS	Small Intestine	intestine

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