Variant report

Variant	rs11718795
Chromosome Location	chr3:47218727-47218728
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	chr3:47216807..47218782-chr3:47220055..47222409,2	K562	blood:
2	chr3:47212127..47215555-chr3:47216166..47219089,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL18-1	chr3:47210139-47219924	NONHSAT089480

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11130114	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130115	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11708451	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11712716	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714282	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11714373	0.89[EUR][1000 genomes]
rs11716539	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719306	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11719738	0.90[EUR][1000 genomes]
rs11923706	0.84[EUR][1000 genomes]
rs12488225	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489211	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493425	0.90[EUR][1000 genomes]
rs12629262	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12635619	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13061071	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13062022	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13063250	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13078131	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13084117	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13091054	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13094438	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13094672	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13098228	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1466740	0.83[EUR][1000 genomes]
rs1466741	0.83[EUR][1000 genomes]
rs1811652	0.90[EUR][1000 genomes]
rs2132173	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276853	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276854	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34103310	0.83[EUR][1000 genomes]
rs4018905	0.86[EUR][1000 genomes]
rs4078466	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4082155	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4682852	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683320	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683324	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57756484	0.86[EUR][1000 genomes]
rs58956475	0.91[EUR][1000 genomes]
rs62246451	0.90[EUR][1000 genomes]
rs62246455	0.87[EUR][1000 genomes]
rs6414436	0.83[EUR][1000 genomes]
rs6442059	0.90[EUR][1000 genomes]
rs6763236	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6766230	0.90[EUR][1000 genomes]
rs6767907	0.89[EUR][1000 genomes]
rs6772670	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773521	0.87[EUR][1000 genomes]
rs6781941	0.85[EUR][1000 genomes]
rs6785790	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6791062	0.88[EUR][1000 genomes]
rs6791842	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6794193	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7615323	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7620997	0.80[EUR][1000 genomes]
rs7621911	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625067	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7625070	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9311403	0.86[EUR][1000 genomes]
rs9812878	0.80[EUR][1000 genomes]
rs9818382	0.90[EUR][1000 genomes]
rs9821119	0.90[EUR][1000 genomes]
rs9837343	0.90[EUR][1000 genomes]
rs9843075	0.86[EUR][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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv3801	chr3:47201530-47246438	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11718795	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11718795	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47206800-47228000	Weak transcription	Spleen	Spleen
2	chr3:47207000-47222400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:47207000-47224400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:47207000-47253800	Weak transcription	Aorta	Aorta
5	chr3:47207200-47219400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:47207200-47220000	Weak transcription	Thymus	Thymus
7	chr3:47207200-47222200	Weak transcription	Fetal Intestine Large	intestine
8	chr3:47207200-47225800	Weak transcription	Placenta	Placenta
9	chr3:47207200-47235800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:47207400-47220800	Weak transcription	HSMMtube	muscle
11	chr3:47207400-47224400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:47207800-47221800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:47207800-47222000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:47207800-47222400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:47207800-47222600	Weak transcription	Small Intestine	intestine
16	chr3:47207800-47223600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:47207800-47224200	Weak transcription	NH-A	brain
18	chr3:47207800-47224800	Weak transcription	Adipose Nuclei	Adipose
19	chr3:47207800-47228000	Weak transcription	HMEC	breast
20	chr3:47208000-47219400	Weak transcription	Pancreas	Pancrea
21	chr3:47208000-47220400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:47208000-47220800	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:47208000-47221000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:47208000-47221600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:47208000-47222000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:47208000-47222000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:47208000-47222000	Weak transcription	NHEK	skin
28	chr3:47208000-47222000	Weak transcription	Osteobl	bone
29	chr3:47208000-47222400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:47208000-47223600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:47208000-47223800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:47208000-47227800	Weak transcription	K562	blood
33	chr3:47208000-47230600	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:47208000-47249600	Weak transcription	Ovary	ovary
35	chr3:47208200-47221000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:47208200-47221200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:47208200-47221800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:47208200-47221800	Weak transcription	Fetal Lung	lung
39	chr3:47208200-47221800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:47208200-47222000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:47208200-47222000	Weak transcription	Primary T cells from cord blood	blood
42	chr3:47208200-47222200	Weak transcription	Brain Anterior Caudate	brain
43	chr3:47208200-47222600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:47208200-47223200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr3:47208200-47223600	Weak transcription	Hela-S3	cervix
46	chr3:47208200-47223800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:47208200-47224200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:47208200-47224600	Weak transcription	Brain Germinal Matrix	brain
49	chr3:47208200-47225200	Weak transcription	Fetal Intestine Small	intestine
50	chr3:47208200-47225400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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