Variant report

Variant	rs13094672
Chromosome Location	chr3:47149439-47149440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47147445..47150358-chr3:47462787..47464363,2	K562	blood:
2	chr3:47148587..47150185-chr3:47152146..47155145,2	K562	blood:

Variant related genes	Relation type
ENSG00000114650	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11130114	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130115	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11708451	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712716	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714282	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11714373	0.88[EUR][1000 genomes]
rs11716539	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11718795	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11719306	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719738	0.88[EUR][1000 genomes]
rs11923706	0.82[EUR][1000 genomes]
rs12488225	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12489211	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12493425	0.88[EUR][1000 genomes]
rs12629262	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12635619	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13061071	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13062022	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13063250	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13078131	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13084117	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13091054	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13094438	0.84[ASN][1000 genomes]
rs13098228	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1466740	0.81[EUR][1000 genomes]
rs1466741	0.81[EUR][1000 genomes]
rs1811652	0.88[EUR][1000 genomes]
rs2132173	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276853	0.84[ASN][1000 genomes]
rs2276854	0.84[ASN][1000 genomes]
rs2385867	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34103310	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4018905	0.87[EUR][1000 genomes]
rs4078466	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4082155	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682852	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683320	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683324	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57756484	0.84[EUR][1000 genomes]
rs58956475	0.87[EUR][1000 genomes]
rs62246451	0.88[EUR][1000 genomes]
rs62246455	0.85[EUR][1000 genomes]
rs6414435	0.81[EUR][1000 genomes]
rs6414436	0.84[EUR][1000 genomes]
rs6442059	0.88[EUR][1000 genomes]
rs6763236	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6766230	0.88[EUR][1000 genomes]
rs6767907	0.88[EUR][1000 genomes]
rs6772670	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6773521	0.85[EUR][1000 genomes]
rs6781941	0.83[EUR][1000 genomes]
rs6785790	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791062	0.87[EUR][1000 genomes]
rs6791842	0.83[ASN][1000 genomes]
rs6794193	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7610636	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7615323	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7621911	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7625067	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625070	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7637302	0.80[ASN][1000 genomes]
rs9311403	0.86[EUR][1000 genomes]
rs9818382	0.88[EUR][1000 genomes]
rs9821119	0.88[EUR][1000 genomes]
rs9837343	0.88[EUR][1000 genomes]
rs9843075	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1002970	chr3:47120592-47170607	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	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
rs13094672	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs13094672	SETD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47098800-47149600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:47110200-47150200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47112400-47153600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:47123000-47159200	Weak transcription	Brain Substantia Nigra	brain
5	chr3:47124600-47154400	Weak transcription	Fetal Brain Male	brain
6	chr3:47125600-47154600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:47125800-47150000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:47125800-47153600	Weak transcription	Esophagus	oesophagus
9	chr3:47125800-47154600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:47125800-47154600	Weak transcription	Gastric	stomach
11	chr3:47125800-47155000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr3:47126000-47153600	Weak transcription	Aorta	Aorta
13	chr3:47126400-47159800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:47126800-47168200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:47128400-47150400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:47135000-47158800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:47137000-47150000	Weak transcription	Ovary	ovary
18	chr3:47139200-47154000	Weak transcription	Brain Anterior Caudate	brain
19	chr3:47139600-47150000	Weak transcription	NHEK	skin
20	chr3:47139600-47153400	Weak transcription	Pancreas	Pancrea
21	chr3:47139600-47154600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:47139600-47161800	Weak transcription	Fetal Brain Female	brain
23	chr3:47139800-47150400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:47139800-47153000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:47139800-47154200	Weak transcription	Colonic Mucosa	Colon
26	chr3:47139800-47163200	Weak transcription	A549	lung
27	chr3:47140000-47175600	Weak transcription	Small Intestine	intestine
28	chr3:47140600-47159200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:47140800-47150200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:47141200-47155000	Weak transcription	HMEC	breast
31	chr3:47141200-47155200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:47143200-47150200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:47143600-47152400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:47143800-47153000	Weak transcription	Fetal Kidney	kidney
35	chr3:47143800-47154600	Weak transcription	Fetal Heart	heart
36	chr3:47144000-47150000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:47144000-47153000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:47144000-47153200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:47144000-47154200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:47144000-47154600	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:47144000-47154600	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:47144200-47150600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:47144200-47155000	Weak transcription	Right Ventricle	heart
44	chr3:47144200-47170800	Weak transcription	Brain Angular Gyrus	brain
45	chr3:47144400-47150600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:47144400-47152200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:47145000-47150400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:47145000-47152600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:47145000-47155000	Strong transcription	GM12878-XiMat	blood
50	chr3:47145200-47150400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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