Variant report

Variant	rs59572954
Chromosome Location	chr18:12996261-12996262
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12989490..12992525-chr18:12992706..12997077,5	MCF-7	breast:
2	chr18:12944429..12952802-chr18:12987284..12998193,21	K562	blood:
3	chr18:12995796..12999639-chr18:13011054..13013784,3	K562	blood:

Variant related genes	Relation type
ENSG00000101639	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000085415	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11080621	0.98[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11080622	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11872263	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11873826	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12232629	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16940054	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16940077	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1786285	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28880030	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35637816	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs473808	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56163906	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57072282	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57607448	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57770092	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58764311	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59385500	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60369117	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61155546	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61610540	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6505778	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7228108	0.88[ASN][1000 genomes]
rs7231935	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7236159	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7239379	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7240309	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7243977	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72874177	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72874185	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72875863	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72875879	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72877625	0.91[EUR][1000 genomes]
rs8086911	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8098299	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8182426	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9303778	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs977104	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9958439	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9959522	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9965066	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1062413	chr18:12988947-13039941	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv543657	chr18:12988947-13039941	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12992000-13000600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr18:12992000-13004400	Weak transcription	Esophagus	oesophagus
3	chr18:12992200-13004800	Weak transcription	Aorta	Aorta
4	chr18:12992400-13000400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:12992400-13000600	Weak transcription	Placenta	Placenta
6	chr18:12992400-13004400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr18:12992600-13000400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr18:12992600-13031200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:12992800-12996400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr18:12992800-12997600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr18:12992800-13004000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr18:12992800-13008800	Weak transcription	Colonic Mucosa	Colon
13	chr18:12992800-13009200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr18:12992800-13013200	Weak transcription	Fetal Kidney	kidney
15	chr18:12992800-13016000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr18:12993000-12996400	Weak transcription	Brain Anterior Caudate	brain
17	chr18:12993000-12997000	Enhancers	HepG2	liver
18	chr18:12993000-13001400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr18:12993000-13006400	Weak transcription	Fetal Brain Female	brain
20	chr18:12993000-13023800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr18:12993200-12996400	Weak transcription	Brain Hippocampus Middle	brain
22	chr18:12993200-13000200	Weak transcription	HSMM	muscle
23	chr18:12993200-13000400	Weak transcription	Adipose Nuclei	Adipose
24	chr18:12993200-13001000	Weak transcription	Fetal Intestine Large	intestine
25	chr18:12993200-13001200	Weak transcription	A549	lung
26	chr18:12993200-13004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr18:12993200-13004800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr18:12993200-13006800	Weak transcription	HSMMtube	muscle
29	chr18:12993200-13007000	Weak transcription	Brain Substantia Nigra	brain
30	chr18:12993200-13008400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr18:12993200-13008400	Weak transcription	Osteobl	bone
32	chr18:12993200-13008800	Weak transcription	NHLF	lung
33	chr18:12993400-12998200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr18:12993400-12998400	Weak transcription	Fetal Lung	lung
35	chr18:12993400-12999400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr18:12993400-12999400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr18:12993400-12999600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr18:12993400-13000200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr18:12993400-13000200	Weak transcription	Liver	Liver
40	chr18:12993400-13000200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr18:12993400-13000200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr18:12993400-13000600	Weak transcription	Fetal Stomach	stomach
43	chr18:12993400-13000800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr18:12993400-13003000	Weak transcription	Fetal Muscle Leg	muscle
45	chr18:12993400-13003800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr18:12993400-13006200	Weak transcription	NH-A	brain
47	chr18:12993400-13006600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr18:12993400-13008200	Weak transcription	Brain Angular Gyrus	brain
49	chr18:12993400-13017800	Weak transcription	Stomach Mucosa	stomach
50	chr18:12993600-13000200	Weak transcription	Primary B cells from cord blood	blood

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