Variant report

Variant	rs12959543
Chromosome Location	chr18:43703899-43703900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43702189..43705091-chr18:43751436..43753812,2	K562	blood:

Variant related genes	Relation type
ENSG00000152242	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11876373	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12604134	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12605796	0.85[ASN][1000 genomes]
rs12606184	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12607480	0.95[ASN][1000 genomes]
rs12954742	0.81[ASN][1000 genomes]
rs12963169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1612622	0.87[ASN][1000 genomes]
rs1620609	0.81[ASN][1000 genomes]
rs1626506	0.81[ASN][1000 genomes]
rs1632043	0.81[ASN][1000 genomes]
rs1658904	0.80[ASN][1000 genomes]
rs1791401	0.82[ASN][1000 genomes]
rs1791406	0.85[ASN][1000 genomes]
rs1791407	0.87[ASN][1000 genomes]
rs1791413	0.81[ASN][1000 genomes]
rs1791414	0.81[ASN][1000 genomes]
rs1791421	0.81[ASN][1000 genomes]
rs1866321	0.81[ASN][1000 genomes]
rs1866322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2467669	0.87[ASN][1000 genomes]
rs2515639	0.87[ASN][1000 genomes]
rs2578184	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2578187	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2578188	0.85[ASN][1000 genomes]
rs2578189	0.87[ASN][1000 genomes]
rs2578190	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2578193	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28372325	0.82[EUR][1000 genomes]
rs28497462	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850644	0.87[ASN][1000 genomes]
rs2852362	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2852363	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2853801	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2853802	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28715068	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28768435	0.95[ASN][1000 genomes]
rs28805990	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28809822	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2886001	0.86[ASN][1000 genomes]
rs35029196	0.86[ASN][1000 genomes]
rs35122885	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35338711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35360831	0.86[ASN][1000 genomes]
rs35657986	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3744992	0.86[ASN][1000 genomes]
rs4243278	0.91[ASN][1000 genomes]
rs4260155	0.88[ASN][1000 genomes]
rs4274509	0.87[ASN][1000 genomes]
rs474878	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890624	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890625	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59082804	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60986007	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6507664	0.81[ASN][1000 genomes]
rs71364518	0.87[ASN][1000 genomes]
rs7226736	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7229971	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7230180	0.95[ASN][1000 genomes]
rs7233665	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8083916	0.95[ASN][1000 genomes]
rs8085233	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8085773	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8088422	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8090410	0.85[ASN][1000 genomes]
rs8096643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9946831	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9952157	0.82[EUR][1000 genomes]
rs9954133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9954534	0.80[EUR][1000 genomes]
rs9954565	0.83[ASN][1000 genomes]
rs9965365	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9965812	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv962965	chr18:43678008-43706302	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43685000-43707000	Weak transcription	Spleen	Spleen
2	chr18:43685000-43709000	Weak transcription	Pancreas	Pancrea
3	chr18:43685200-43704200	Weak transcription	Psoas Muscle	Psoas
4	chr18:43685200-43704800	Weak transcription	Placenta	Placenta
5	chr18:43685200-43709000	Weak transcription	Right Ventricle	heart
6	chr18:43685200-43712600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr18:43685200-43712600	Weak transcription	Stomach Mucosa	stomach
8	chr18:43685200-43715200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr18:43685200-43735600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr18:43685400-43704200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr18:43685400-43704800	Weak transcription	Brain Substantia Nigra	brain
12	chr18:43685400-43704800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr18:43685400-43708200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr18:43685400-43709800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr18:43685400-43710600	Weak transcription	Colonic Mucosa	Colon
16	chr18:43685400-43711200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr18:43685400-43711600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr18:43685400-43714800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr18:43685400-43714800	Weak transcription	NHDF-Ad	bronchial
20	chr18:43685400-43717200	Weak transcription	HepG2	liver
21	chr18:43685400-43729000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr18:43685400-43732200	Weak transcription	Fetal Kidney	kidney
23	chr18:43686000-43710200	Weak transcription	NHEK	skin
24	chr18:43686400-43711400	Weak transcription	Fetal Brain Male	brain
25	chr18:43686600-43708200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr18:43688200-43705400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr18:43689600-43705000	Weak transcription	Gastric	stomach
28	chr18:43690000-43715600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr18:43690600-43705000	Weak transcription	Brain Germinal Matrix	brain
30	chr18:43693200-43711000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr18:43693200-43712200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr18:43693400-43710400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr18:43693800-43710200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr18:43694200-43709600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr18:43694200-43713600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr18:43694200-43714000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:43694200-43715600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr18:43694600-43717400	Weak transcription	Brain Anterior Caudate	brain
39	chr18:43694800-43704800	Weak transcription	Esophagus	oesophagus
40	chr18:43694800-43708800	Weak transcription	Lung	lung
41	chr18:43694800-43709600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr18:43695000-43705000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr18:43695000-43714800	Weak transcription	HSMMtube	muscle
44	chr18:43695000-43715200	Weak transcription	K562	blood
45	chr18:43695200-43704600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr18:43695200-43704600	Weak transcription	Left Ventricle	heart
47	chr18:43695200-43704800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr18:43695200-43705400	Weak transcription	Osteobl	bone
49	chr18:43695200-43705800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr18:43695200-43707400	Weak transcription	GM12878-XiMat	blood

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