Variant report

Variant	rs3885902
Chromosome Location	chr18:11858572-11858573
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	POLR2A	chr18:11857099-11860426	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr18:11848810-11859649	IMR90	lung:	n/a	n/a
3	POLR2A	chr18:11857027-11860404	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr18:11849742-11860299	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr18:11856977-11859646	A549	lung:	n/a	n/a
6	MYC	chr18:11857026-11858596	MCF10A-Er-Src	breast:	n/a	chr18:11857779-11857790 chr18:11857779-11857790
7	TBP	chr18:11857027-11860429	Hela-S3	cervix:	n/a	chr18:11858437-11858448
8	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	chr18:11857778..11858710-chr5:179050165..179050756,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000272703	TF binding region
ENSG00000267165	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000255112	Chromatin interaction
ENSG00000165527	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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16976742	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16976749	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4371220	1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5018698	1.00[ASN][1000 genomes]
rs5018699	1.00[ASN][1000 genomes]
rs5018701	1.00[ASN][1000 genomes]
rs5018702	1.00[ASN][1000 genomes]
rs5018703	1.00[ASN][1000 genomes]
rs5018704	1.00[ASN][1000 genomes]
rs61462499	1.00[ASN][1000 genomes]
rs62097389	0.91[ASN][1000 genomes]
rs715688	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7228231	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7241172	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7241199	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7241336	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73409587	1.00[ASN][1000 genomes]
rs73409590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73944918	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73944920	1.00[EUR][1000 genomes];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:89 , 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	chr18:11855600-11858600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr18:11855600-11859000	Weak transcription	Primary T cells from cord blood	blood
19	chr18:11855600-11880800	Weak transcription	Fetal Brain Female	brain
20	chr18:11856400-11858800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr18:11856600-11859200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr18:11856600-11859200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr18:11856600-11861600	Weak transcription	Gastric	stomach
24	chr18:11856600-11865000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr18:11856800-11858600	Active TSS	A549	lung
26	chr18:11857000-11859400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr18:11857000-11860800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr18:11857400-11858800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr18:11857400-11859400	Active TSS	Psoas Muscle	Psoas
30	chr18:11857400-11860200	Weak transcription	Small Intestine	intestine
31	chr18:11857600-11858600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr18:11857600-11859200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr18:11857600-11860000	Active TSS	Hela-S3	cervix
34	chr18:11857600-11860800	Enhancers	HUVEC	blood vessel
35	chr18:11857600-11860800	Enhancers	Osteobl	bone
36	chr18:11857600-11872800	Weak transcription	Left Ventricle	heart
37	chr18:11857800-11858600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr18:11857800-11858600	Enhancers	Adipose Nuclei	Adipose
39	chr18:11857800-11858800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr18:11857800-11858800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr18:11857800-11858800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr18:11857800-11858800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr18:11857800-11858800	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr18:11857800-11859000	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr18:11857800-11859200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr18:11857800-11859200	Weak transcription	Placenta	Placenta
47	chr18:11857800-11859400	Weak transcription	Colonic Mucosa	Colon
48	chr18:11857800-11859400	Weak transcription	Esophagus	oesophagus
49	chr18:11857800-11859400	Weak transcription	Lung	lung
50	chr18:11857800-11859400	Enhancers	HSMM	muscle

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