Variant report

Variant	rs9961827
Chromosome Location	chr18:12883777-12883778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:65596946..65598700-chr18:12882626..12885488,2	MCF-7	breast:
2	chr11:75110573..75111082-chr18:12883776..12884593,2	Hela-S3	cervix:
3	chr18:12774117..12776643-chr18:12883699..12885836,3	K562	blood:
4	chr18:12843323..12846138-chr18:12882410..12884352,2	MCF-7	breast:
5	chr1:84971759..84972422-chr18:12883583..12884223,2	Hela-S3	cervix:
6	chr18:12880282..12885478-chr18:12946145..12950206,8	K562	blood:
7	chr12:6875531..6876528-chr18:12883727..12884284,2	Hela-S3	cervix:
8	chr18:12699803..12702594-chr18:12881299..12884040,2	K562	blood:
9	chr18:12882667..12884316-chr18:13724618..13726583,2	K562	blood:
10	chr18:12883748..12884411-chr5:137878834..137879510,2	Hela-S3	cervix:
11	chr18:12702487..12704134-chr18:12881395..12884232,2	MCF-7	breast:
12	chr18:12883574..12884321-chr19:1269204..1269887,2	Hela-S3	cervix:
13	chr1:28907896..28908672-chr18:12883704..12884487,2	Hela-S3	cervix:
14	chr18:12883550..12884300-chr8:22084933..22085873,2	Hela-S3	cervix:
15	chr18:12869114..12870887-chr18:12882231..12883982,2	K562	blood:
16	chr18:12882771..12885367-chr18:12946819..12949664,2	MCF-7	breast:
17	chr18:12883600..12884285-chr19:40596090..40596674,2	HCT-116	colon:
18	chr18:12699667..12702594-chr18:12881299..12884281,3	K562	blood:
19	chr18:12880282..12884361-chr18:12946145..12949673,9	K562	blood:
20	chr17:8076499..8077007-chr18:12883737..12884359,2	Hela-S3	cervix:
21	chr1:145382262..145383113-chr18:12883770..12884685,2	Hela-S3	cervix:
22	chr18:12882295..12883903-chr18:12953395..12955724,2	K562	blood:
23	chr18:12808897..12811465-chr18:12881476..12883993,2	MCF-7	breast:
24	chr18:12883650..12884263-chrX:109245703..109246214,2	Hela-S3	cervix:
25	chr18:12657085..12659648-chr18:12882376..12884207,2	K562	blood:
26	chr1:147806040..147807089-chr18:12883758..12884527,3	Hela-S3	cervix:
27	chr18:12827164..12830026-chr18:12882449..12884069,2	K562	blood:
28	chr18:12881395..12884200-chr18:12946697..12949759,6	MCF-7	breast:
29	chr18:12883270..12884142-chr5:34838946..34839489,2	HCT-116	colon:

No data

Variant related genes	Relation type
ENSG00000200463	Chromatin interaction
ENSG00000175354	Chromatin interaction
ENSG00000168490	Chromatin interaction
ENSG00000269296	Chromatin interaction
ENSG00000099622	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000202408	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000260302	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000159335	Chromatin interaction
ENSG00000149273	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000205838	Chromatin interaction
ENSG00000272323	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000157600	Chromatin interaction
ENSG00000197782	Chromatin interaction
ENSG00000197989	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000120705	Chromatin interaction
ENSG00000177150	Chromatin interaction
ENSG00000215527	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2292758	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3826556	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs45579734	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs471401	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4797708	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs507304	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56384328	0.85[ASN][1000 genomes]
rs578377	0.81[EUR][1000 genomes]
rs58200120	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59471125	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs607906	0.82[ASN][1000 genomes]
rs60803113	0.85[ASN][1000 genomes]
rs622717	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs637643	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6505769	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs669822	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs670671	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs683468	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7238238	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7241650	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72872144	0.84[ASN][1000 genomes]
rs73950683	0.82[ASN][1000 genomes]
rs73950684	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73950685	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8084365	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8091305	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8098730	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9954778	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9959061	0.85[EUR][1000 genomes]
rs9961931	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9966378	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv909407	chr18:12877060-12917703	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	n/a
7	esv3433183	chr18:12883052-12885400	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12882200-12885000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr18:12882200-12885000	Active TSS	A549	lung
3	chr18:12882200-12885000	Active TSS	HMEC	breast
4	chr18:12882200-12885000	Active TSS	NHLF	lung
5	chr18:12882400-12884600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr18:12882400-12884600	Active TSS	Fetal Thymus	thymus
7	chr18:12882400-12885000	Active TSS	GM12878-XiMat	blood
8	chr18:12882400-12885200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr18:12882400-12885600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr18:12882600-12883800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr18:12882600-12884200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr18:12882600-12884600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr18:12882600-12884600	Active TSS	Muscle Satellite Cultured Cells	--
14	chr18:12882600-12884600	Active TSS	Fetal Muscle Leg	muscle
15	chr18:12882600-12884600	Active TSS	Thymus	Thymus
16	chr18:12882600-12884600	Active TSS	HSMM	muscle
17	chr18:12882600-12884800	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr18:12882600-12884800	Active TSS	Psoas Muscle	Psoas
19	chr18:12882600-12885000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr18:12882600-12885000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr18:12882600-12885000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr18:12882600-12885000	Active TSS	Fetal Stomach	stomach
23	chr18:12882600-12885000	Active TSS	NHDF-Ad	bronchial
24	chr18:12882800-12883800	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr18:12882800-12883800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr18:12882800-12883800	Active TSS	Right Atrium	heart
27	chr18:12882800-12884200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr18:12882800-12884600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr18:12882800-12884600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr18:12882800-12884600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr18:12882800-12884800	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr18:12882800-12884800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr18:12882800-12884800	Active TSS	Stomach Mucosa	stomach
34	chr18:12882800-12885000	Active TSS	H9 Cell Line	embryonic stem cell
35	chr18:12882800-12885000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr18:12882800-12885000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr18:12882800-12885000	Active TSS	Fetal Intestine Small	intestine
38	chr18:12882800-12885000	Active TSS	Placenta	Placenta
39	chr18:12882800-12885200	Active TSS	Colonic Mucosa	Colon
40	chr18:12883000-12883800	Bivalent/Poised TSS	HepG2	liver
41	chr18:12883000-12884400	Active TSS	Dnd41	blood
42	chr18:12883000-12884600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr18:12883000-12884600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr18:12883000-12884600	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr18:12883000-12884600	Active TSS	Primary T cells from cord blood	blood
46	chr18:12883000-12884600	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr18:12883000-12884800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr18:12883000-12884800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:12883000-12884800	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr18:12883000-12884800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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