Variant report

Variant	rs3826612
Chromosome Location	chr18:29523919-29523920
allele	A/C
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	chr18:29522074-29524311	GM12878	blood:	n/a	n/a
2	MAX	chr18:29522858-29523953	SK-N-SH	brain:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
3	POLR2A	chr18:29522017-29524380	HepG2	liver:	n/a	n/a
4	FOXA1	chr18:29523638-29524069	HepG2	liver:	n/a	n/a
5	TEAD4	chr18:29522725-29524272	ECC-1	luminal epithelium:	n/a	chr18:29522963-29522972
6	TEAD4	chr18:29522815-29523930	ECC-1	luminal epithelium:	n/a	chr18:29522963-29522972
7	MXI1	chr18:29522044-29523995	HepG2	liver:	n/a	n/a
8	MYC	chr18:29522286-29524727	K562	blood:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
9	BHLHE40	chr18:29522137-29523985	HepG2	liver:	n/a	chr18:29523112-29523125 chr18:29523114-29523123 chr18:29523115-29523124 chr18:29523108-29523129 chr18:29523114-29523123 chr18:29522742-29522758
10	MAX	chr18:29522825-29523934	MCF-7	breast:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
11	MAX	chr18:29522181-29524200	K562	blood:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
12	RELA	chr18:29522151-29524136	GM18505	blood:	n/a	n/a
13	MAX	chr18:29522727-29524027	HCT-116	colon:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
14	MXI1	chr18:29522235-29524175	Hela-S3	cervix:	n/a	n/a
15	REST	chr18:29522017-29524007	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr18:29522180-29523945	HL-60	blood:	n/a	n/a
17	MXI1	chr18:29521941-29523997	IMR90	lung:	n/a	n/a
18	PML	chr18:29522003-29523964	GM12878	blood:	n/a	n/a
19	MAX	chr18:29522784-29523922	HUVEC	blood vessel:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
20	MAX	chr18:29522826-29523949	A549	lung:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
21	FOXA1	chr18:29523537-29524096	HepG2	liver:	n/a	n/a
22	MAX	chr18:29522826-29523987	SK-N-SH	brain:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
23	MAX	chr18:29522805-29524039	ECC-1	luminal epithelium:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
24	MAX	chr18:29522730-29524013	HepG2	liver:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
25	FOXA1	chr18:29523621-29523920	T-47D	breast:	n/a	n/a
26	POLR2A	chr18:29522474-29523950	HepG2	liver:	n/a	n/a
27	FOXA1	chr18:29523577-29524014	HepG2	liver:	n/a	n/a
28	MYC	chr18:29522856-29524033	NB4	blood:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
29	POLR2A	chr18:29522015-29523929	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr18:29522768-29524048	ECC-1	luminal epithelium:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
31	CHD1	chr18:29523610-29524255	H1-hESC	embryonic stem cell:	n/a	n/a
32	TEAD4	chr18:29523318-29524189	HepG2	liver:	n/a	n/a
33	HCFC1	chr18:29521847-29524057	Hela-S3	cervix:	n/a	n/a
34	MAX	chr18:29522638-29524069	HepG2	liver:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
35	FOXA2	chr18:29523657-29524068	HepG2	liver:	n/a	n/a
36	MYC	chr18:29523019-29524380	MCF10A-Er-Src	breast:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
37	MAZ	chr18:29522171-29523949	IMR90	lung:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
38	POLR2A	chr18:29522271-29524169	GM12878	blood:	n/a	n/a
39	MAX	chr18:29522453-29524051	HCT-116	colon:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
40	MAZ	chr18:29522203-29523920	K562	blood:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
41	TEAD4	chr18:29522690-29523937	K562	blood:	n/a	chr18:29522963-29522972
42	MXI1	chr18:29521978-29525320	SK-N-SH	brain:	n/a	n/a
43	REST	chr18:29522333-29524064	HL-60	blood:	n/a	n/a
44	MYC	chr18:29522774-29524191	K562	blood:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
45	MAX	chr18:29522228-29523930	GM12878	blood:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
46	ELF1	chr18:29522703-29523946	GM12878	blood:	n/a	chr18:29523206-29523217 chr18:29523207-29523216
47	FOXA1	chr18:29523581-29524014	T-47D	breast:	n/a	n/a
48	JUN	chr18:29521820-29525062	K562	blood:	n/a	chr18:29524927-29524938 chr18:29524884-29524893 chr18:29523238-29523247 chr18:29523904-29523913 chr18:29523903-29523912 chr18:29524929-29524937
49	SPI1	chr18:29522742-29524071	HL-60	blood:	n/a	chr18:29523170-29523179 chr18:29523163-29523176 chr18:29523770-29523783 chr18:29523529-29523542
50	MAX	chr18:29522754-29524035	A549	lung:	n/a	chr18:29523105-29523121 chr18:29523114-29523123

No.	Distal block	Cell Line	Cell type
1	chr18:29523882..29525586-chr18:29646566..29649385,2	K562	blood:
2	chr18:29517111..29520943-chr18:29521139..29523956,5	MCF-7	breast:
3	chr18:29522249..29524505-chr18:29596603..29599089,2	MCF-7	breast:
4	chr18:29521939..29525237-chr18:29670716..29673913,4	MCF-7	breast:
5	chr17:48942638..48944565-chr18:29522050..29524653,2	MCF-7	breast:
6	chr18:29518719..29521005-chr18:29521192..29525426,5	MCF-7	breast:
7	chr18:29521665..29524441-chr18:29544834..29547590,2	K562	blood:
8	chr18:29521618..29525019-chr18:29670361..29672184,4	MCF-7	breast:
9	chr18:29521537..29525393-chr18:29670839..29674328,7	K562	blood:
10	chr18:29520857..29524705-chr18:29670705..29674434,7	K562	blood:
11	chr18:29468408..29471507-chr18:29523062..29524905,3	K562	blood:
12	chr18:29523716..29526205-chr18:29536614..29539662,3	K562	blood:

Variant related genes	Relation type
TRAPPC8	TF binding region
ENSG00000153339	Chromatin interaction
ENSG00000101695	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000263917	Chromatin interaction
ENSG00000134758	Chromatin interaction
ENSG00000265008	Chromatin interaction
ENSG00000222320	Chromatin interaction
ENSG00000266105	Chromatin interaction
ENSG00000141232	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10468902	0.81[ASN][1000 genomes]
rs10853415	0.86[ASN][1000 genomes]
rs10853416	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11662341	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12604640	0.83[ASN][1000 genomes]
rs12957331	0.86[ASN][1000 genomes]
rs12969126	0.86[ASN][1000 genomes]
rs1680643	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35203717	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3865397	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4513172	0.84[ASN][1000 genomes]
rs5011500	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs521491	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs549818	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs563247	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs614342	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6506944	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6506945	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506946	0.88[ASN][1000 genomes]
rs675570	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7229979	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7230326	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7239098	0.84[ASN][1000 genomes]
rs7239951	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8088396	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs930018	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9958368	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9966530	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431975	chr18:29311034-29527902	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1067252	chr18:29475073-29583744	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29520200-29526800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr18:29521000-29524400	Active TSS	Psoas Muscle	Psoas
3	chr18:29521200-29524200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr18:29521200-29524400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr18:29521200-29524400	Active TSS	GM12878-XiMat	blood
6	chr18:29521200-29524800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr18:29521200-29524800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr18:29521200-29525200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr18:29521400-29524000	Active TSS	Ovary	ovary
10	chr18:29521400-29524000	Active TSS	NHDF-Ad	bronchial
11	chr18:29521400-29524000	Active TSS	NHLF	lung
12	chr18:29521400-29524200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:29521400-29524200	Active TSS	HSMM	muscle
14	chr18:29521400-29524400	Active TSS	Fetal Kidney	kidney
15	chr18:29521400-29524600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:29521400-29524600	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr18:29521400-29525000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr18:29521400-29525400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr18:29521600-29524000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr18:29521600-29524000	Active TSS	Aorta	Aorta
21	chr18:29521600-29524000	Active TSS	Fetal Intestine Small	intestine
22	chr18:29521600-29524200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr18:29521600-29524200	Active TSS	Fetal Intestine Large	intestine
24	chr18:29521600-29524200	Active TSS	Right Ventricle	heart
25	chr18:29521600-29524200	Active TSS	A549	lung
26	chr18:29521600-29524800	Active TSS	H1 Cell Line	embryonic stem cell
27	chr18:29521600-29524800	Active TSS	HSMMtube	muscle
28	chr18:29521600-29525400	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr18:29521800-29524000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr18:29521800-29524000	Active TSS	Fetal Heart	heart
31	chr18:29521800-29524000	Active TSS	K562	blood
32	chr18:29521800-29524200	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr18:29521800-29524200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr18:29521800-29524400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr18:29521800-29524400	Active TSS	Fetal Muscle Trunk	muscle
36	chr18:29521800-29524600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr18:29521800-29524600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr18:29522000-29524000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr18:29522000-29524000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr18:29522000-29524000	Active TSS	Esophagus	oesophagus
41	chr18:29522000-29524000	Active TSS	Gastric	stomach
42	chr18:29522000-29524000	Active TSS	Left Ventricle	heart
43	chr18:29522000-29524000	Active TSS	Pancreas	Pancrea
44	chr18:29522000-29524000	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr18:29522000-29524200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr18:29522000-29524200	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr18:29522000-29524400	Active TSS	Brain Anterior Caudate	brain
48	chr18:29522000-29524600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr18:29522000-29524600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr18:29522000-29524800	Active TSS	H9 Cell Line	embryonic stem cell

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