Variant report

Variant	rs11716539
Chromosome Location	chr3:47186503-47186504
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47184671..47186867-chr3:47196509..47199504,2	MCF-7	breast:
2	chr3:47184823..47187568-chr3:47200664..47202534,2	K562	blood:
3	chr3:47185004..47187148-chr3:47202667..47204488,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NBEAL2-2	chr3:47185663-47186830	l_2362_chr3:47180551-47192368_testes

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11130114	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130115	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708451	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712716	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714282	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714373	0.90[EUR][1000 genomes]
rs11718795	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719306	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719738	0.91[EUR][1000 genomes]
rs11923706	0.85[EUR][1000 genomes]
rs12488225	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12489211	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12493425	0.91[EUR][1000 genomes]
rs12629262	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12635619	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13061071	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13062022	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063250	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13078131	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13084117	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091054	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13094438	0.85[ASN][1000 genomes]
rs13094672	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13098228	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1466740	0.84[EUR][1000 genomes]
rs1466741	0.84[EUR][1000 genomes]
rs1811652	0.91[EUR][1000 genomes]
rs2132173	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276853	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2276854	0.85[ASN][1000 genomes]
rs34103310	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4018905	0.88[EUR][1000 genomes]
rs4078466	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4082155	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683320	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683322	0.80[EUR][1000 genomes]
rs4683324	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57756484	0.87[EUR][1000 genomes]
rs58956475	0.90[EUR][1000 genomes]
rs62246451	0.91[EUR][1000 genomes]
rs62246455	0.88[EUR][1000 genomes]
rs6414435	0.80[EUR][1000 genomes]
rs6414436	0.84[EUR][1000 genomes]
rs6442055	0.80[EUR][1000 genomes]
rs6442059	0.91[EUR][1000 genomes]
rs6763236	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766230	0.91[EUR][1000 genomes]
rs6767907	0.90[EUR][1000 genomes]
rs6772670	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773521	0.88[EUR][1000 genomes]
rs6777145	0.80[EUR][1000 genomes]
rs6781941	0.86[EUR][1000 genomes]
rs6785790	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6791062	0.89[EUR][1000 genomes]
rs6791842	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6794193	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7610636	0.81[EUR][1000 genomes]
rs7615323	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620997	0.81[EUR][1000 genomes]
rs7621911	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625067	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7625070	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9311403	0.87[EUR][1000 genomes]
rs9812878	0.81[EUR][1000 genomes]
rs9818382	0.91[EUR][1000 genomes]
rs9821119	0.91[EUR][1000 genomes]
rs9837343	0.91[EUR][1000 genomes]
rs9843075	0.87[EUR][1000 genomes]
rs9854790	0.80[EUR][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	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	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11716539	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs11716539	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47165800-47187000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:47165800-47191000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:47165800-47197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:47166000-47200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:47166000-47201200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:47166000-47204600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:47166200-47197200	Weak transcription	Aorta	Aorta
8	chr3:47166200-47200600	Weak transcription	Hela-S3	cervix
9	chr3:47166400-47194200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:47166600-47204200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:47167400-47202400	Weak transcription	HSMM	muscle
12	chr3:47167800-47187600	Weak transcription	Fetal Stomach	stomach
13	chr3:47167800-47195400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:47173600-47191000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:47175800-47200400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:47176400-47190800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:47177800-47194200	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:47178000-47190800	Weak transcription	Right Ventricle	heart
19	chr3:47178000-47194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:47178600-47187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:47178600-47188200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:47178600-47190600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:47180000-47188400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr3:47181000-47193600	Weak transcription	Fetal Heart	heart
25	chr3:47181200-47188200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr3:47182000-47190600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:47182000-47192600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:47182000-47195400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:47182600-47190800	Weak transcription	Small Intestine	intestine
30	chr3:47182600-47200800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:47182800-47187000	Weak transcription	Right Atrium	heart
32	chr3:47182800-47191000	Weak transcription	Pancreas	Pancrea
33	chr3:47182800-47192000	Weak transcription	Stomach Mucosa	stomach
34	chr3:47182800-47198200	Weak transcription	Primary B cells from cord blood	blood
35	chr3:47183400-47189000	Enhancers	Primary T cells fromperipheralblood	blood
36	chr3:47183600-47192000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:47183600-47193800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:47183600-47200800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:47183600-47202200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:47183800-47187000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:47183800-47187000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:47183800-47190600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:47183800-47191000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:47183800-47191000	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:47183800-47193800	Weak transcription	Primary T cells from cord blood	blood
46	chr3:47183800-47194000	Weak transcription	Dnd41	blood
47	chr3:47183800-47194200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:47183800-47194400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:47183800-47198000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:47183800-47202200	Weak transcription	NHEK	skin

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