Variant report

Variant	rs7241199
Chromosome Location	chr18:11857066-11857067
allele	C/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	SP1	chr18:11856884-11857970	A549	lung:	n/a	chr18:11857575-11857589
2	NR3C1	chr18:11856977-11857910	A549	lung:	n/a	chr18:11857109-11857125
3	MAX	chr18:11857013-11857985	ECC-1	luminal epithelium:	n/a	chr18:11857779-11857790 chr18:11857779-11857790
4	FOSL1	chr18:11857003-11858057	HCT-116	colon:	n/a	n/a
5	SP1	chr18:11856988-11858038	HCT-116	colon:	n/a	chr18:11857575-11857589
6	TEAD4	chr18:11857052-11857923	ECC-1	luminal epithelium:	n/a	n/a
7	ATF3	chr18:11857061-11857860	A549	lung:	n/a	n/a
8	STAT3	chr18:11857029-11857902	Hela-S3	cervix:	n/a	n/a
9	BACH1	chr18:11857025-11857968	H1-hESC	embryonic stem cell:	n/a	chr18:11857896-11857910
10	MYBL2	chr18:11857065-11857804	HepG2	liver:	n/a	n/a
11	GATA3	chr18:11857050-11857970	A549	lung:	n/a	n/a
12	MXI1	chr18:11857015-11858286	Hela-S3	cervix:	n/a	n/a
13	SRF	chr18:11857053-11858043	HCT-116	colon:	n/a	n/a
14	TEAD4	chr18:11857049-11857746	K562	blood:	n/a	n/a
15	SP1	chr18:11856978-11858002	A549	lung:	n/a	chr18:11857575-11857589
16	BCL3	chr18:11857015-11857901	A549	lung:	n/a	n/a
17	SRF	chr18:11856996-11857992	ECC-1	luminal epithelium:	n/a	n/a
18	CEBPB	chr18:11857003-11857446	A549	lung:	n/a	chr18:11857250-11857261
19	SIN3AK20	chr18:11857045-11857958	HCT-116	colon:	n/a	n/a
20	REST	chr18:11856999-11857973	A549	lung:	n/a	n/a
21	POLR2A	chr18:11848810-11859649	IMR90	lung:	n/a	n/a
22	FOXM1	chr18:11856907-11857993	ECC-1	luminal epithelium:	n/a	n/a
23	EP300	chr18:11856962-11857917	ECC-1	luminal epithelium:	n/a	chr18:11857095-11857109 chr18:11857370-11857377 chr18:11857291-11857298
24	JUN	chr18:11856998-11858565	K562	blood:	n/a	n/a
25	TEAD4	chr18:11857005-11857978	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr18:11856971-11858013	U87	brain:	n/a	n/a
27	SIN3AK20	chr18:11857052-11857960	HCT-116	colon:	n/a	n/a
28	MAX	chr18:11856962-11858042	ECC-1	luminal epithelium:	n/a	chr18:11857779-11857790 chr18:11857779-11857790
29	POLR2A	chr18:11857027-11860404	Hela-S3	cervix:	n/a	n/a
30	BRCA1	chr18:11857013-11857945	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr18:11857065-11857872	U87	brain:	n/a	n/a
32	POLR2A	chr18:11849742-11860299	MCF10A-Er-Src	breast:	n/a	n/a
33	NR3C1	chr18:11856969-11857885	A549	lung:	n/a	chr18:11857109-11857125
34	FOSL2	chr18:11856966-11858047	A549	lung:	n/a	n/a
35	SP1	chr18:11856906-11858043	HCT-116	colon:	n/a	chr18:11857575-11857589
36	TCF12	chr18:11856828-11858095	ECC-1	luminal epithelium:	n/a	chr18:11857167-11857176
37	EP300	chr18:11856937-11858013	A549	lung:	n/a	chr18:11857095-11857109 chr18:11857370-11857377 chr18:11857291-11857298
38	NR3C1	chr18:11857054-11857402	ECC-1	luminal epithelium:	n/a	chr18:11857109-11857125
39	EP300	chr18:11856918-11857904	ECC-1	luminal epithelium:	n/a	chr18:11857095-11857109 chr18:11857370-11857377 chr18:11857291-11857298
40	CEBPB	chr18:11857040-11857735	ECC-1	luminal epithelium:	n/a	chr18:11857250-11857261
41	MAX	chr18:11857013-11858048	A549	lung:	n/a	chr18:11857779-11857790 chr18:11857779-11857790
42	CBX3	chr18:11857029-11857924	HCT-116	colon:	n/a	n/a
43	MAX	chr18:11857044-11857993	HepG2	liver:	n/a	chr18:11857779-11857790 chr18:11857779-11857790
44	POLR2A	chr18:11856977-11859646	A549	lung:	n/a	n/a
45	NR3C1	chr18:11856956-11857934	A549	lung:	n/a	chr18:11857109-11857125
46	EP300	chr18:11856939-11858052	A549	lung:	n/a	chr18:11857095-11857109 chr18:11857370-11857377 chr18:11857291-11857298
47	MYC	chr18:11856931-11858033	MCF10A-Er-Src	breast:	n/a	chr18:11857779-11857790 chr18:11857779-11857790
48	POLR2A	chr18:11857059-11858252	Hela-S3	cervix:	n/a	n/a
49	FOXM1	chr18:11856862-11857977	ECC-1	luminal epithelium:	n/a	n/a
50	MAX	chr18:11857022-11858092	HCT-116	colon:	n/a	chr18:11857779-11857790 chr18:11857779-11857790

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:11848600..11852886-chr18:11853629..11859008,5	K562	blood:

Variant related genes	Relation type
GNAL	TF binding region
ENSG00000267165	TF binding region
ENSG00000255112	Chromatin interaction
ENSG00000267165	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11875788	1.00[CEU][hapmap]
rs1249628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16976742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16976746	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs16976749	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3885902	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4371220	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs5018698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018703	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018704	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61462499	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62097389	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs715688	1.00[ASN][1000 genomes]
rs7228231	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7234436	1.00[CEU][hapmap]
rs7239927	1.00[CEU][hapmap]
rs7240842	1.00[CEU][hapmap]
rs7241172	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]
rs7241336	0.91[ASN][1000 genomes]
rs7244948	1.00[CEU][hapmap]
rs73409587	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409590	1.00[ASN][1000 genomes]
rs73944918	0.95[ASN][1000 genomes]
rs73944920	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11852400-11857200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:11852400-11860000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:11852400-11880800	Weak transcription	Aorta	Aorta
4	chr18:11853400-11857400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:11853400-11859200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr18:11853600-11857400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr18:11853600-11857400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:11853600-11857400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr18:11853600-11857400	Weak transcription	Fetal Muscle Leg	muscle
10	chr18:11853600-11857600	Weak transcription	Fetal Thymus	thymus
11	chr18:11853600-11859200	Weak transcription	Right Ventricle	heart
12	chr18:11853600-11859600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr18:11853600-11883800	Weak transcription	Ovary	ovary
14	chr18:11853800-11857200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr18:11853800-11857200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr18:11853800-11857200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr18:11853800-11857200	Weak transcription	Brain Anterior Caudate	brain
18	chr18:11853800-11857200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr18:11853800-11857200	Weak transcription	Fetal Kidney	kidney
20	chr18:11853800-11857200	Weak transcription	K562	blood
21	chr18:11853800-11857400	Weak transcription	Placenta	Placenta
22	chr18:11853800-11857400	Weak transcription	Right Atrium	heart
23	chr18:11853800-11861000	Weak transcription	Fetal Lung	lung
24	chr18:11853800-11884200	Weak transcription	Brain Substantia Nigra	brain
25	chr18:11854000-11857200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr18:11854000-11857200	Weak transcription	Left Ventricle	heart
27	chr18:11854000-11861600	Weak transcription	Spleen	Spleen
28	chr18:11854000-11875000	Weak transcription	Brain Hippocampus Middle	brain
29	chr18:11854000-11884200	Weak transcription	Brain Angular Gyrus	brain
30	chr18:11854200-11857400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr18:11854200-11868200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr18:11854400-11868400	Weak transcription	Primary B cells from cord blood	blood
33	chr18:11854800-11889200	Weak transcription	Fetal Brain Male	brain
34	chr18:11855000-11857200	Weak transcription	Colon Smooth Muscle	Colon
35	chr18:11855200-11857800	Strong transcription	Brain Germinal Matrix	brain
36	chr18:11855200-11857800	Weak transcription	Thymus	Thymus
37	chr18:11855400-11857600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr18:11855400-11858200	Enhancers	Fetal Intestine Large	intestine
39	chr18:11855400-11860200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr18:11855400-11875400	Weak transcription	Fetal Stomach	stomach
41	chr18:11855600-11857200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr18:11855600-11857200	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr18:11855600-11857400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr18:11855600-11857400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr18:11855600-11858600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr18:11855600-11859000	Weak transcription	Primary T cells from cord blood	blood
47	chr18:11855600-11880800	Weak transcription	Fetal Brain Female	brain
48	chr18:11855800-11858200	Enhancers	Stomach Mucosa	stomach
49	chr18:11856000-11857200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr18:11856000-11857200	Enhancers	HSMM	muscle

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