Variant report

Variant	rs13062022
Chromosome Location	chr3:47169375-47169376
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	chr3:47164535..47167910-chr3:47168833..47170750,3	K562	blood:
2	chr3:47160235..47164319-chr3:47167866..47171765,6	K562	blood:

Variant related genes	Relation type
ENSG00000181555	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11130114	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130115	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712716	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714282	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714373	0.90[EUR][1000 genomes]
rs11716539	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718795	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719306	0.89[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	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12489211	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12493425	0.91[EUR][1000 genomes]
rs12629262	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12635619	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13061071	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13063250	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13078131	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13084117	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091054	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13094438	0.85[ASN][1000 genomes]
rs13094672	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13098228	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1466740	0.83[EUR][1000 genomes]
rs1466741	0.83[EUR][1000 genomes]
rs1811652	0.91[EUR][1000 genomes]
rs2132173	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276853	0.85[ASN][1000 genomes]
rs2276854	0.85[ASN][1000 genomes]
rs34103310	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4018905	0.88[EUR][1000 genomes]
rs4078466	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4082155	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682852	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683320	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683322	0.80[EUR][1000 genomes]
rs4683324	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57756484	0.86[EUR][1000 genomes]
rs58956475	0.90[EUR][1000 genomes]
rs62246451	0.91[EUR][1000 genomes]
rs62246455	0.87[EUR][1000 genomes]
rs6414435	0.81[EUR][1000 genomes]
rs6414436	0.85[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	0.91[EUR][1000 genomes]
rs6772670	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773521	0.87[EUR][1000 genomes]
rs6777145	0.80[EUR][1000 genomes]
rs6781941	0.85[EUR][1000 genomes]
rs6785790	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6791062	0.89[EUR][1000 genomes]
rs6791842	0.84[ASN][1000 genomes]
rs6794193	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7610636	0.80[EUR][1000 genomes]
rs7615323	0.90[AMR][1000 genomes];0.95[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]
rs7623888	0.80[EUR][1000 genomes]
rs7625067	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7625070	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9311403	0.88[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: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
rs13062022	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs13062022	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47140000-47175600	Weak transcription	Small Intestine	intestine
2	chr3:47144200-47170800	Weak transcription	Brain Angular Gyrus	brain
3	chr3:47145800-47175000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:47155200-47172600	Weak transcription	Colonic Mucosa	Colon
5	chr3:47155400-47183800	Weak transcription	Esophagus	oesophagus
6	chr3:47162600-47170000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:47163000-47169800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:47164000-47176000	Weak transcription	Right Atrium	heart
9	chr3:47165000-47172000	Weak transcription	Fetal Heart	heart
10	chr3:47165600-47175000	Weak transcription	Psoas Muscle	Psoas
11	chr3:47165800-47169400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:47165800-47169600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:47165800-47169600	Weak transcription	Gastric	stomach
14	chr3:47165800-47169600	Weak transcription	Pancreas	Pancrea
15	chr3:47165800-47170400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:47165800-47171400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:47165800-47171800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:47165800-47175000	Weak transcription	Left Ventricle	heart
19	chr3:47165800-47175200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:47165800-47175200	Weak transcription	HUVEC	blood vessel
21	chr3:47165800-47175600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:47165800-47175600	Weak transcription	Right Ventricle	heart
23	chr3:47165800-47176000	Weak transcription	Spleen	Spleen
24	chr3:47165800-47177200	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:47165800-47187000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:47165800-47191000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:47165800-47197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:47166000-47169400	Weak transcription	NHEK	skin
29	chr3:47166000-47169600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:47166000-47169600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:47166000-47169600	Weak transcription	Osteobl	bone
32	chr3:47166000-47169800	Weak transcription	Brain Anterior Caudate	brain
33	chr3:47166000-47169800	Weak transcription	NH-A	brain
34	chr3:47166000-47170000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:47166000-47170000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:47166000-47170000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:47166000-47170000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:47166000-47170000	Weak transcription	NHDF-Ad	bronchial
39	chr3:47166000-47170800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:47166000-47170800	Weak transcription	Brain Substantia Nigra	brain
41	chr3:47166000-47171000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:47166000-47171600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:47166000-47171800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:47166000-47172400	Weak transcription	Fetal Brain Male	brain
45	chr3:47166000-47173400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:47166000-47174400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:47166000-47175000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:47166000-47175000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:47166000-47175400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:47166000-47175400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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