Variant report

Variant	rs639457
Chromosome Location	chr18:12005438-12005439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr18:12005257-12005522	MCF10A-Er-Src	breast:	n/a	n/a
2	RUNX3	chr18:12005253-12005510	GM12878	blood:	n/a	n/a
3	RUNX3	chr18:12005200-12005522	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:11978843..11982198-chr18:12003396..12007810,5	MCF-7	breast:
2	chr18:12000492..12002135-chr18:12004782..12007391,2	MCF-7	breast:
3	chr18:11993441..11996170-chr18:12004399..12006022,2	MCF-7	breast:
4	chr18:11849319..11851808-chr18:12002886..12005709,2	MCF-7	breast:
5	chr18:11980368..11983094-chr18:12003809..12006804,4	MCF-7	breast:

No data

Variant related genes	Relation type
IMPA2	TF binding region
ENSG00000255112	Chromatin interaction
ENSG00000266955	Chromatin interaction
ENSG00000141401	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1249977	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1265916	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4352114	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4555213	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs626097	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505704	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505705	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505706	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs663401	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs671470	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs672917	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs686961	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7234493	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7244276	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7244661	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9955803	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9955982	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9956089	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription 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	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS 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	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv909393	chr18:12001258-12155371	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
2	chr18:11993400-12016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr18:11995600-12014400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr18:11996000-12005600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr18:11996200-12005600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr18:11996200-12012200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr18:11996200-12014800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr18:11996200-12015400	Weak transcription	Brain Anterior Caudate	brain
9	chr18:11996400-12007800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr18:11996600-12035000	Weak transcription	Primary T cells from cord blood	blood
11	chr18:11996800-12017200	Weak transcription	Fetal Thymus	thymus
12	chr18:11996800-12034400	Weak transcription	Primary B cells from cord blood	blood
13	chr18:11997000-12034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr18:11998400-12006000	Weak transcription	Brain Angular Gyrus	brain
15	chr18:11998400-12013200	Weak transcription	Right Atrium	heart
16	chr18:11998400-12014400	Weak transcription	Psoas Muscle	Psoas
17	chr18:11998400-12015200	Weak transcription	Brain Hippocampus Middle	brain
18	chr18:11998400-12034000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr18:11998600-12010000	Weak transcription	Colon Smooth Muscle	Colon
20	chr18:11998800-12005600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr18:11998800-12029400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr18:11999000-12006800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr18:11999000-12017400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr18:11999000-12019200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr18:11999000-12019400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr18:11999000-12019400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr18:11999000-12034000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr18:11999000-12035400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr18:11999200-12008400	Weak transcription	Fetal Kidney	kidney
30	chr18:11999200-12012600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr18:11999200-12015400	Weak transcription	HSMM	muscle
32	chr18:11999200-12035800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr18:11999800-12008400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr18:11999800-12008400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr18:11999800-12012600	Weak transcription	Brain Germinal Matrix	brain
36	chr18:11999800-12014400	Weak transcription	Fetal Brain Female	brain
37	chr18:11999800-12015600	Weak transcription	HSMMtube	muscle
38	chr18:12000000-12005800	Weak transcription	Right Ventricle	heart
39	chr18:12000800-12018400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr18:12001600-12006400	Weak transcription	Gastric	stomach
41	chr18:12001800-12005600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr18:12001800-12005600	Weak transcription	Ovary	ovary
43	chr18:12001800-12009600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr18:12001800-12009800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr18:12002000-12005600	Weak transcription	Liver	Liver
46	chr18:12002000-12006200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr18:12002000-12008400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr18:12002000-12009800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr18:12002000-12013000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr18:12002000-12013600	Weak transcription	Thymus	Thymus

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