Variant report

Variant	rs2304952
Chromosome Location	chr18:11908720-11908721
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	ELF1	chr18:11908016-11908784	K562	blood:	n/a	chr18:11908444-11908456 chr18:11908343-11908354
2	BCLAF1	chr18:11908000-11909062	GM12878	blood:	n/a	chr18:11908598-11908611
3	E2F6	chr18:11908199-11909132	K562	blood:	n/a	chr18:11908713-11908720 chr18:11908404-11908416 chr18:11908710-11908721 chr18:11908713-11908720 chr18:11908404-11908413 chr18:11908709-11908721 chr18:11908713-11908720 chr18:11909055-11909070 chr18:11908446-11908456 chr18:11908920-11908935
4	RCOR1	chr18:11908039-11908844	Hela-S3	cervix:	n/a	n/a
5	SIN3AK20	chr18:11908087-11909052	H1-hESC	embryonic stem cell:	n/a	n/a
6	ELF1	chr18:11907866-11908954	HCT-116	colon:	n/a	chr18:11908922-11908931 chr18:11908444-11908456 chr18:11908343-11908354
7	MAX	chr18:11908146-11908917	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr18:11908591-11908781	GM19238	blood:	n/a	n/a
9	YY1	chr18:11908576-11908777	HCT-116	colon:	n/a	chr18:11908599-11908610
10	CTCF	chr18:11908580-11908730	HUVEC	blood vessel:	n/a	n/a
11	TAF1	chr18:11907998-11909067	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr18:11908046-11909302	HepG2	liver:	n/a	n/a
13	ELF1	chr18:11907996-11909196	GM12878	blood:	n/a	chr18:11908922-11908931 chr18:11908444-11908456 chr18:11908343-11908354
14	POLR2A	chr18:11907986-11909065	GM12892	blood:	n/a	n/a
15	EBF1	chr18:11908098-11908891	GM12878	blood:	n/a	n/a
16	GABPA	chr18:11908097-11909119	H1-hESC	embryonic stem cell:	n/a	chr18:11908810-11908819 chr18:11908404-11908413
17	TCF12	chr18:11908204-11908891	A549	lung:	n/a	n/a
18	POLR2A	chr18:11908094-11909155	Hela-S3	cervix:	n/a	n/a
19	RELA	chr18:11908097-11908855	GM15510	blood:	n/a	n/a
20	MTA3	chr18:11907879-11909796	GM12878	blood:	n/a	n/a
21	E2F1	chr18:11908155-11908964	Hela-S3	cervix:	n/a	chr18:11908713-11908720 chr18:11908404-11908416 chr18:11908713-11908720 chr18:11908404-11908413 chr18:11908709-11908721 chr18:11908713-11908720 chr18:11908446-11908456 chr18:11908920-11908935
22	PAX5	chr18:11908157-11908748	GM12878	blood:	n/a	chr18:11908465-11908492 chr18:11908362-11908371
23	CCNT2	chr18:11908140-11909117	K562	blood:	n/a	n/a
24	ZBTB7A	chr18:11908184-11909156	K562	blood:	n/a	n/a
25	MYC	chr18:11908140-11909169	NB4	blood:	n/a	n/a
26	GTF2F1	chr18:11908673-11908723	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr18:11908086-11909118	A549	lung:	n/a	n/a
28	POU2F2	chr18:11907998-11908860	GM12878	blood:	n/a	n/a
29	SPI1	chr18:11908100-11908894	GM12878	blood:	n/a	chr18:11908343-11908352 chr18:11908341-11908354 chr18:11908342-11908355
30	POLR2A	chr18:11908103-11909331	GM12878	blood:	n/a	n/a
31	TCF12	chr18:11908102-11908892	GM12878	blood:	n/a	n/a
32	POLR2A	chr18:11908095-11908912	K562	blood:	n/a	n/a
33	PML	chr18:11908225-11908771	MCF-7	breast:	n/a	n/a
34	POLR2A	chr18:11908165-11909093	A549	lung:	n/a	n/a
35	BCLAF1	chr18:11908015-11908934	GM12878	blood:	n/a	chr18:11908598-11908611
36	POLR2A	chr18:11908034-11909826	GM18505	blood:	n/a	n/a
37	POLR2A	chr18:11908059-11909173	GM12878	blood:	n/a	n/a
38	POLR2A	chr18:11908039-11909690	GM18951	blood:	n/a	n/a
39	CTCF	chr18:11908680-11908830	GM12871	blood:	n/a	n/a
40	SIN3AK20	chr18:11908103-11908880	MCF-7	breast:	n/a	n/a
41	ZNF263	chr18:11908065-11908829	K562	blood:	n/a	n/a
42	E2F4	chr18:11908179-11909023	K562	blood:	n/a	chr18:11908713-11908720 chr18:11908404-11908416 chr18:11908713-11908720 chr18:11908404-11908413 chr18:11908709-11908721 chr18:11908713-11908720 chr18:11908446-11908456 chr18:11908920-11908935
43	E2F6	chr18:11908606-11908908	A549	lung:	n/a	chr18:11908713-11908720 chr18:11908710-11908721 chr18:11908713-11908720 chr18:11908709-11908721 chr18:11908713-11908720
44	E2F6	chr18:11908447-11909014	H1-hESC	embryonic stem cell:	n/a	chr18:11908713-11908720 chr18:11908710-11908721 chr18:11908713-11908720 chr18:11908709-11908721 chr18:11908713-11908720 chr18:11908920-11908935
45	MAX	chr18:11908113-11909235	K562	blood:	n/a	n/a
46	RCOR1	chr18:11908111-11908828	HepG2	liver:	n/a	n/a
47	POLR2A	chr18:11908131-11908896	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr18:11908022-11909322	Hela-S3	cervix:	n/a	n/a
49	ZKSCAN1	chr18:11908163-11908761	Hela-S3	cervix:	n/a	n/a
50	TBP	chr18:11908129-11908783	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr18:11908695-11908745	Hepatocyte	liver:	n/a
2	chr18:11908695-11908745	SAEC	small airway:	n/a
3	chr18:11908695-11908745	GM12891	blood:	n/a
4	chr18:11908695-11908745	ECC-1	luminal epithelium:	n/a
5	chr18:11908695-11908745	HMEC	breast:	n/a
6	chr18:11908695-11908745	CMK	blood:	n/a
7	chr18:11908695-11908745	NHBE	bronchial:	n/a
8	chr18:11908695-11908745	PrEC	prostate:	n/a
9	chr18:11908695-11908745	SKMC	muscle:	n/a
10	chr18:11908695-11908745	HCM	heart:	n/a
11	chr18:11908695-11908745	HRCEpiC	kidney:	n/a
12	chr18:11908695-11908745	NB4	blood:	n/a
13	chr18:11908695-11908745	HepG2	liver:	n/a
14	chr18:11908695-11908745	A549	lung:	n/a
15	chr18:11908695-11908745	HPAEpiC	pulmonary alveolar:	n/a
16	chr18:11908695-11908745	Hela-S3	cervix:	n/a
17	chr18:11908695-11908745	HNPCEpiC	eye:	n/a
18	chr18:11908695-11908745	MCF-7	breast:	n/a
19	chr18:11908695-11908745	IMR90	lung:	fetal
20	chr18:11908695-11908745	SK-N-SH_RA	brain:	n/a
21	chr18:11908695-11908745	U87	brain:	n/a
22	chr18:11908695-11908745	NHDF-neo	bronchial:	n/a
23	chr18:11908695-11908745	HUVEC	blood vessel:	n/a
24	chr18:11908695-11908745	ProgFib	skin:	n/a
25	chr18:11908695-11908745	AG10803	skin:	n/a
26	chr18:11908695-11908745	Jurkat	blood:	n/a
27	chr18:11908695-11908745	AG09309	skin:	n/a
28	chr18:11908695-11908745	SK-N-SH	brain:	n/a
29	chr18:11908695-11908745	HCF	heart:	n/a
30	chr18:11908695-11908745	GM12878	blood:	n/a
31	chr18:11908695-11908745	BJ	skin:	n/a
32	chr18:11908695-11908745	LNCaP	prostate:	n/a
33	chr18:11908695-11908745	AG04449	skin:	fetal
34	chr18:11908695-11908745	ovcar-3	ovarian:	n/a
35	chr18:11908695-11908745	PANC-1	pancreas:	n/a
36	chr18:11908695-11908745	NH-A	brain:	n/a
37	chr18:11908695-11908745	HRPEpiC	eye:	n/a
38	chr18:11908695-11908745	AG09319	gingival:	n/a
39	chr18:11908695-11908745	K562	blood:	n/a
40	chr18:11908695-11908745	HL-60	blood:	n/a
41	chr18:11908695-11908745	HIPEpiC	eye:	n/a
42	chr18:11908695-11908745	GM06990	blood:	n/a
43	chr18:11908695-11908745	HCT-116	colon:	n/a
44	chr18:11908695-11908745	Caco-2	colon:	n/a
45	chr18:11908695-11908745	HAEpiC	amniotic membrane:	n/a
46	chr18:11908695-11908745	GM12892	blood:	n/a
47	chr18:11908695-11908745	HCPEpiC	choroid plexus:	n/a
48	chr18:11908695-11908745	PFSK-1	brain:	n/a
49	chr18:11908695-11908745	AG04450	lung:	fetal
50	chr18:11908695-11908745	NT2-D1	testis:	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:11908518..11911302-chr18:12009524..12011140,2	MCF-7	breast:
2	chr18:11848334..11851734-chr18:11906595..11909240,3	K562	blood:
3	chr18:11906925..11910950-chr18:11978930..11983753,7	MCF-7	breast:
4	chr18:11908077..11908808-chr3:73160102..73160621,2	Hela-S3	cervix:
5	chr17:8076437..8076995-chr18:11908144..11908909,2	Hela-S3	cervix:
6	chr14:100842502..100843242-chr18:11908364..11908922,2	Hela-S3	cervix:
7	chr18:11906869..11908788-chr18:11979428..11982249,2	K562	blood:
8	chr18:11848894..11852838-chr18:11907232..11909901,3	MCF-7	breast:
9	chr18:11907153..11910661-chr18:11980045..11982514,4	MCF-7	breast:
10	chr12:56550673..56553390-chr18:11908435..11911361,2	MCF-7	breast:
11	chr18:11899627..11904640-chr18:11906955..11910092,5	MCF-7	breast:
12	chr10:75543773..75546549-chr18:11908703..11911397,2	MCF-7	breast:
13	chr18:11899621..11904572-chr18:11905422..11909871,7	K562	blood:
14	chr18:11853727..11856399-chr18:11905762..11908760,2	K562	blood:
15	chr18:11885563..11889310-chr18:11906331..11909961,4	MCF-7	breast:
16	chr18:11851217..11853122-chr18:11907362..11910210,4	MCF-7	breast:
17	chr18:11901497..11903544-chr18:11908058..11909728,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNAL-1	chr18:11908711-11909222	ENSG00000273141.1

Variant related genes	Relation type
MPPE1	TF binding region
MPPE1	CpG island
ENSG00000176473	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000140105	Chromatin interaction
ENSG00000267165	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000154889	Chromatin interaction
ENSG00000255112	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000141401	Chromatin interaction
ENSG00000200463	Chromatin interaction
ENSG00000214655	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs8091142	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833590	chr18:11757329-11924539	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv1059775	chr18:11892845-11911143	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv909383	chr18:11904266-11926730	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 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	chr18:11907000-11909200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:11907200-11909200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr18:11907200-11909200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr18:11907200-11909200	Active TSS	Rectal Smooth Muscle	rectum
5	chr18:11907200-11909600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr18:11907200-11909600	Active TSS	Right Atrium	heart
7	chr18:11907400-11909200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr18:11907400-11909200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr18:11907400-11909200	Active TSS	Fetal Kidney	kidney
10	chr18:11907400-11909600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:11907600-11909000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr18:11907600-11909000	Active TSS	Brain Germinal Matrix	brain
13	chr18:11907600-11909000	Active TSS	HMEC	breast
14	chr18:11907600-11909200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr18:11907600-11909200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr18:11907600-11909200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr18:11907600-11909200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr18:11907600-11909200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr18:11907600-11909200	Active TSS	Primary T cells from cord blood	blood
20	chr18:11907600-11909200	Active TSS	Brain Substantia Nigra	brain
21	chr18:11907600-11909200	Active TSS	Esophagus	oesophagus
22	chr18:11907600-11909200	Active TSS	Fetal Heart	heart
23	chr18:11907600-11909200	Active TSS	Gastric	stomach
24	chr18:11907600-11909200	Active TSS	Left Ventricle	heart
25	chr18:11907600-11909200	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr18:11907600-11909200	Active TSS	K562	blood
27	chr18:11907600-11909400	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr18:11907600-11909400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr18:11907600-11909400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr18:11907600-11909400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr18:11907600-11909400	Active TSS	Ovary	ovary
32	chr18:11907600-11909400	Active TSS	GM12878-XiMat	blood
33	chr18:11907600-11909400	Active TSS	HSMM	muscle
34	chr18:11907600-11909400	Active TSS	NHDF-Ad	bronchial
35	chr18:11907600-11909600	Active TSS	H1 Cell Line	embryonic stem cell
36	chr18:11907600-11909600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:11907600-11909600	Active TSS	Duodenum Mucosa	Duodenum
38	chr18:11907600-11909600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr18:11907600-11909600	Active TSS	Psoas Muscle	Psoas
40	chr18:11907600-11909800	Active TSS	HSMMtube	muscle
41	chr18:11907600-11910000	Active TSS	Colonic Mucosa	Colon
42	chr18:11907800-11909000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr18:11907800-11909000	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr18:11907800-11909000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr18:11907800-11909000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr18:11907800-11909000	Active TSS	Dnd41	blood
47	chr18:11907800-11909200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:11907800-11909200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr18:11907800-11909200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr18:11907800-11909200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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