Variant report

Variant	rs3809911
Chromosome Location	chr18:12947360-12947361
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	chr18:12947307-12948778	GM15510	blood:	n/a	n/a
2	REST	chr18:12947171-12948830	HL-60	blood:	n/a	chr18:12947999-12948012 chr18:12948495-12948508 chr18:12948486-12948499
3	POLR2A	chr18:12946718-12949058	K562	blood:	n/a	n/a
4	POLR2A	chr18:12946772-12947739	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr18:12946826-12949126	HepG2	liver:	n/a	n/a
6	MAX	chr18:12947073-12947660	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF384	chr18:12946683-12947691	K562	blood:	n/a	n/a
8	MYC	chr18:12946836-12948845	K562	blood:	n/a	chr18:12948057-12948066 chr18:12948452-12948461 chr18:12948452-12948461 chr18:12948453-12948460 chr18:12947967-12947977
9	POLR2A	chr18:12946961-12948903	HL-60	blood:	n/a	n/a
10	MAX	chr18:12946630-12949025	HepG2	liver:	n/a	chr18:12948057-12948066 chr18:12948452-12948461 chr18:12948452-12948461 chr18:12948453-12948460 chr18:12947967-12947977
11	POLR2A	chr18:12944542-12947768	K562	blood:	n/a	n/a
12	POLR2A	chr18:12946981-12948835	GM12878	blood:	n/a	n/a
13	EP300	chr18:12946589-12947785	ECC-1	luminal epithelium:	n/a	chr18:12947122-12947136 chr18:12947126-12947135
14	POLR2A	chr18:12947332-12947753	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr18:12946838-12948804	K562	blood:	n/a	n/a
16	RCOR1	chr18:12946926-12947728	GM12878	blood:	n/a	n/a
17	CHD2	chr18:12947316-12947793	GM12878	blood:	n/a	n/a
18	POLR2A	chr18:12947082-12948789	GM19193	blood:	n/a	n/a
19	POLR2A	chr18:12946770-12948850	K562	blood:	n/a	n/a
20	MAZ	chr18:12946534-12949045	IMR90	lung:	n/a	chr18:12948057-12948066 chr18:12948452-12948461 chr18:12948452-12948461 chr18:12948453-12948460 chr18:12947967-12947977
21	RCOR1	chr18:12946579-12948733	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr18:12947351-12948707	HCT-116	colon:	n/a	n/a
23	STAT5A	chr18:12947337-12947747	GM12878	blood:	n/a	n/a
24	POLR2A	chr18:12947277-12948705	HCT-116	colon:	n/a	n/a
25	POLR2A	chr18:12947028-12948947	PFSK-1	brain:	n/a	n/a
26	MXI1	chr18:12946619-12948978	IMR90	lung:	n/a	n/a
27	POLR2A	chr18:12947253-12948840	H1-neurons	neurons:	n/a	n/a
28	SIN3A	chr18:12947232-12947708	GM12878	blood:	n/a	n/a
29	SMARCB1	chr18:12946966-12948773	Hela-S3	cervix:	n/a	n/a
30	ZKSCAN1	chr18:12946693-12947649	Hela-S3	cervix:	n/a	n/a
31	MAX	chr18:12947306-12948865	HUVEC	blood vessel:	n/a	chr18:12948057-12948066 chr18:12948452-12948461 chr18:12948452-12948461 chr18:12948453-12948460 chr18:12947967-12947977
32	POLR2A	chr18:12946782-12947757	PFSK-1	brain:	n/a	n/a
33	NFIC	chr18:12946596-12947378	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr18:12947336-12947720	GM12891	blood:	n/a	n/a
35	HDAC2	chr18:12947331-12947712	HepG2	liver:	n/a	n/a
36	POLR2A	chr18:12947090-12948792	Gliobla	brain:	n/a	n/a
37	MYBL2	chr18:12946634-12947718	HepG2	liver:	n/a	n/a
38	POLR2A	chr18:12946907-12948770	K562	blood:	n/a	n/a
39	POLR2A	chr18:12947212-12947762	GM12878	blood:	n/a	n/a
40	TEAD4	chr18:12947328-12947766	K562	blood:	n/a	n/a
41	TCF12	chr18:12946597-12947794	ECC-1	luminal epithelium:	n/a	chr18:12946818-12946828 chr18:12947468-12947478 chr18:12946888-12946896
42	SIN3AK20	chr18:12946760-12947820	K562	blood:	n/a	n/a
43	SIN3AK20	chr18:12946739-12948882	HCT-116	colon:	n/a	n/a
44	ELF1	chr18:12947276-12948599	MCF-7	breast:	n/a	chr18:12948063-12948072 chr18:12948072-12948081 chr18:12948503-12948512 chr18:12948065-12948077
45	MAX	chr18:12946669-12949025	A549	lung:	n/a	chr18:12948057-12948066 chr18:12948452-12948461 chr18:12948452-12948461 chr18:12948453-12948460 chr18:12947967-12947977
46	EGR1	chr18:12947331-12948727	K562	blood:	n/a	chr18:12947994-12948005 chr18:12948435-12948444 chr18:12947962-12947975 chr18:12948281-12948295 chr18:12947996-12948005 chr18:12947958-12947980 chr18:12948277-12948290 chr18:12947961-12947976 chr18:12948280-12948295 chr18:12947962-12947975 chr18:12947993-12948007 chr18:12947709-12947723 chr18:12947992-12948007 chr18:12947995-12948005 chr18:12947993-12948006 chr18:12947964-12947974 chr18:12947999-12948012 chr18:12947967-12947977 chr18:12947993-12948006 chr18:12948281-12948294 chr18:12947993-12948006 chr18:12947645-12947659 chr18:12947964-12947974 chr18:12947962-12947976 chr18:12947989-12948011 chr18:12947993-12948006 chr18:12947963-12947974 chr18:12947995-12948005
47	NFIC	chr18:12946626-12947679	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr18:12946778-12948829	PBDE	blood:	n/a	n/a
49	MXI1	chr18:12946574-12949059	SK-N-SH	brain:	n/a	n/a
50	BHLHE40	chr18:12946873-12947649	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12947032..12947845-chr19:10304947..10305817,2	Hela-S3	cervix:
2	chr18:12881395..12884200-chr18:12946697..12949759,6	MCF-7	breast:
3	chr18:12946715..12947712-chr20:44563153..44563778,2	Hela-S3	cervix:
4	chr18:12946771..12949148-chr18:13055556..13057689,2	K562	blood:
5	chr18:12928157..12929851-chr18:12946775..12948725,2	K562	blood:
6	chr18:12700182..12704223-chr18:12944670..12949511,9	K562	blood:
7	chr18:12928762..12931382-chr18:12946071..12947896,2	MCF-7	breast:
8	chr18:12373949..12378992-chr18:12946352..12949410,8	K562	blood:
9	chr18:12880282..12884361-chr18:12946145..12949673,9	K562	blood:
10	chr18:12946986..12949410-chr18:12970714..12972312,2	MCF-7	breast:
11	chr18:12946237..12948654-chr18:13006557..13008669,3	K562	blood:
12	chr18:12946883..12949783-chr18:12990489..12993346,5	MCF-7	breast:
13	chr18:12836738..12838821-chr18:12946925..12949352,2	K562	blood:
14	chr18:12701407..12705081-chr18:12945993..12949483,5	MCF-7	breast:
15	chr18:12880282..12885478-chr18:12946145..12950206,8	K562	blood:
16	chr18:12376943..12379295-chr18:12946308..12947818,2	K562	blood:
17	chr18:12944429..12952802-chr18:12987284..12998193,21	K562	blood:
18	chr18:12700812..12705381-chr18:12946243..12950219,9	K562	blood:
19	chr18:12882771..12885367-chr18:12946819..12949664,2	MCF-7	breast:
20	chr18:12945719..12950670-chr18:12989123..12995651,19	K562	blood:
21	chr1:28974722..28975572-chr18:12946882..12947646,2	Hela-S3	cervix:
22	chr18:12375798..12379149-chr18:12946624..12949226,4	MCF-7	breast:
23	chr18:12945869..12950267-chr18:12985686..12992743,10	MCF-7	breast:

Variant related genes	Relation type
SEH1L	TF binding region
ENSG00000085415	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000130816	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000100982	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000175354	Chromatin interaction
ENSG00000101639	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12162175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9949863	1.00[ASN][1000 genomes]
rs9960379	1.00[ASN][1000 genomes]
rs9964794	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	esv3450694	chr18:12933001-12955144	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
10	esv3342017	chr18:12946977-12949725	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
11	esv3446919	chr18:12947052-12949000	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 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	chr18:12946200-12947600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr18:12946200-12949000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr18:12946200-12949200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr18:12946200-12949400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr18:12946400-12947600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr18:12946400-12947600	Flanking Active TSS	Fetal Thymus	thymus
7	chr18:12946400-12948400	Active TSS	GM12878-XiMat	blood
8	chr18:12946400-12948400	Active TSS	HMEC	breast
9	chr18:12946400-12948800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:12946400-12948800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:12946400-12949000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr18:12946400-12949000	Active TSS	HSMMtube	muscle
13	chr18:12946400-12949200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr18:12946400-12949200	Active TSS	K562	blood
15	chr18:12946400-12949400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr18:12946400-12949400	Active TSS	HSMM	muscle
17	chr18:12946600-12947400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr18:12946600-12947400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr18:12946600-12947400	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr18:12946600-12947400	Flanking Active TSS	NH-A	brain
21	chr18:12946600-12947600	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr18:12946600-12947600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr18:12946600-12947600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr18:12946600-12947600	Flanking Active TSS	HUVEC	blood vessel
25	chr18:12946600-12947600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr18:12946600-12948400	Active TSS	Muscle Satellite Cultured Cells	--
27	chr18:12946600-12948400	Active TSS	NHLF	lung
28	chr18:12946600-12948600	Active TSS	Fetal Intestine Large	intestine
29	chr18:12946600-12948600	Active TSS	Right Ventricle	heart
30	chr18:12946600-12948600	Active TSS	Hela-S3	cervix
31	chr18:12946600-12948600	Active TSS	HepG2	liver
32	chr18:12946600-12948600	Active TSS	NHDF-Ad	bronchial
33	chr18:12946600-12948800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr18:12946600-12948800	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr18:12946600-12948800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr18:12946600-12949000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr18:12946600-12949000	Active TSS	H1 Cell Line	embryonic stem cell
38	chr18:12946600-12949000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr18:12946600-12949000	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr18:12946600-12949000	Active TSS	A549	lung
41	chr18:12946600-12949200	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr18:12946600-12949200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr18:12946600-12949200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr18:12946600-12949400	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr18:12946600-12949400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr18:12946800-12947400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr18:12946800-12947400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr18:12946800-12947400	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr18:12946800-12947400	Flanking Active TSS	Fetal Lung	lung
50	chr18:12946800-12947400	Flanking Active TSS	Rectal Smooth Muscle	rectum

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