Variant report

Variant	rs61462499
Chromosome Location	chr18:11858902-11858903
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	chr18:11857099-11860426	Hela-S3	cervix:	n/a	n/a
2	MYC	chr18:11858855-11859055	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr18:11848810-11859649	IMR90	lung:	n/a	n/a
4	POLR2A	chr18:11857027-11860404	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr18:11849742-11860299	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr18:11858812-11860404	Hela-S3	cervix:	n/a	n/a
7	RFX5	chr18:11858632-11860480	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr18:11856977-11859646	A549	lung:	n/a	n/a
9	RCOR1	chr18:11858658-11860512	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr18:11858746-11859009	Hela-S3	cervix:	n/a	n/a
11	TBP	chr18:11857027-11860429	Hela-S3	cervix:	n/a	chr18:11858437-11858448
12	POLR2A	chr18:11858831-11858967	A549	lung:	n/a	n/a
13	POLR2A	chr18:11849706-11860430	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:11848600..11852886-chr18:11853629..11859008,5	K562	blood:
2	chr14:50359621..50360261-chr18:11858407..11859233,2	Hela-S3	cervix:
3	chr18:11740510..11743051-chr18:11858756..11861303,2	K562	blood:

Variant related genes	Relation type
ENSG00000272703	TF binding region
ENSG00000255112	Chromatin interaction
ENSG00000165527	Chromatin interaction
ENSG00000267165	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1249628	0.95[ASN][1000 genomes]
rs16976742	0.95[ASN][1000 genomes]
rs16976749	1.00[ASN][1000 genomes]
rs3885902	1.00[ASN][1000 genomes]
rs4371220	0.91[ASN][1000 genomes]
rs5018698	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018699	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018701	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018702	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018703	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018704	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62097389	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs715688	1.00[ASN][1000 genomes]
rs7228231	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7241172	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7241199	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7241336	0.91[ASN][1000 genomes]
rs73409587	0.93[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:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11852400-11860000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr18:11852400-11880800	Weak transcription	Aorta	Aorta
3	chr18:11853400-11859200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr18:11853600-11859200	Weak transcription	Right Ventricle	heart
5	chr18:11853600-11859600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr18:11853600-11883800	Weak transcription	Ovary	ovary
7	chr18:11853800-11861000	Weak transcription	Fetal Lung	lung
8	chr18:11853800-11884200	Weak transcription	Brain Substantia Nigra	brain
9	chr18:11854000-11861600	Weak transcription	Spleen	Spleen
10	chr18:11854000-11875000	Weak transcription	Brain Hippocampus Middle	brain
11	chr18:11854000-11884200	Weak transcription	Brain Angular Gyrus	brain
12	chr18:11854200-11868200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr18:11854400-11868400	Weak transcription	Primary B cells from cord blood	blood
14	chr18:11854800-11889200	Weak transcription	Fetal Brain Male	brain
15	chr18:11855400-11860200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr18:11855400-11875400	Weak transcription	Fetal Stomach	stomach
17	chr18:11855600-11859000	Weak transcription	Primary T cells from cord blood	blood
18	chr18:11855600-11880800	Weak transcription	Fetal Brain Female	brain
19	chr18:11856600-11859200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr18:11856600-11859200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr18:11856600-11861600	Weak transcription	Gastric	stomach
22	chr18:11856600-11865000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr18:11857000-11859400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr18:11857000-11860800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr18:11857400-11859400	Active TSS	Psoas Muscle	Psoas
26	chr18:11857400-11860200	Weak transcription	Small Intestine	intestine
27	chr18:11857600-11859200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr18:11857600-11860000	Active TSS	Hela-S3	cervix
29	chr18:11857600-11860800	Enhancers	HUVEC	blood vessel
30	chr18:11857600-11860800	Enhancers	Osteobl	bone
31	chr18:11857600-11872800	Weak transcription	Left Ventricle	heart
32	chr18:11857800-11859000	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr18:11857800-11859200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr18:11857800-11859200	Weak transcription	Placenta	Placenta
35	chr18:11857800-11859400	Weak transcription	Colonic Mucosa	Colon
36	chr18:11857800-11859400	Weak transcription	Esophagus	oesophagus
37	chr18:11857800-11859400	Weak transcription	Lung	lung
38	chr18:11857800-11859400	Enhancers	HSMM	muscle
39	chr18:11857800-11859600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr18:11857800-11859800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr18:11857800-11860000	Weak transcription	HSMMtube	muscle
42	chr18:11857800-11860200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr18:11857800-11860400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr18:11857800-11860600	Enhancers	NHDF-Ad	bronchial
45	chr18:11857800-11861000	Enhancers	Duodenum Mucosa	Duodenum
46	chr18:11857800-11861200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr18:11857800-11861400	Weak transcription	Right Atrium	heart
48	chr18:11857800-11861800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr18:11857800-11862800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr18:11857800-11866000	Weak transcription	Brain Anterior Caudate	brain

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