Variant report

Variant	rs11923706
Chromosome Location	chr3:47161214-47161215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47160235..47164319-chr3:47167866..47171765,6	K562	blood:
2	chr3:47150417..47152283-chr3:47160822..47163333,2	MCF-7	breast:
3	chr3:47160775..47162844-chr3:47166336..47168539,2	MCF-7	breast:
4	chr3:47160419..47162941-chr3:47203566..47205231,2	K562	blood:
5	chr3:47144584..47146288-chr3:47160200..47162965,2	K562	blood:
6	chr3:47160899..47162845-chr3:47163476..47165450,2	K562	blood:

Variant related genes	Relation type
ENSG00000181555	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10433549	0.85[ASN][1000 genomes]
rs11130114	0.85[EUR][1000 genomes]
rs11130115	0.85[EUR][1000 genomes]
rs11707736	0.91[ASN][1000 genomes]
rs11708451	0.85[EUR][1000 genomes]
rs11709660	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11712716	0.85[EUR][1000 genomes]
rs11713693	0.91[ASN][1000 genomes]
rs11714373	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11715121	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11716539	0.85[EUR][1000 genomes]
rs11718795	0.84[EUR][1000 genomes]
rs11719306	0.84[EUR][1000 genomes]
rs11719738	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11720139	0.85[ASN][1000 genomes]
rs11917361	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11920354	0.81[ASN][1000 genomes]
rs12488225	0.82[EUR][1000 genomes]
rs12489211	0.82[EUR][1000 genomes]
rs12493425	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12629262	0.85[EUR][1000 genomes]
rs12631730	0.82[ASN][1000 genomes]
rs12635619	0.83[EUR][1000 genomes]
rs12715421	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13061071	0.82[EUR][1000 genomes]
rs13062022	0.85[EUR][1000 genomes]
rs13084117	0.85[EUR][1000 genomes]
rs13094672	0.82[EUR][1000 genomes]
rs13098228	0.82[EUR][1000 genomes]
rs1466740	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1466741	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17784127	0.89[ASN][1000 genomes]
rs1811652	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278963	0.86[ASN][1000 genomes]
rs2305635	0.87[ASN][1000 genomes]
rs4018905	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682852	0.85[EUR][1000 genomes]
rs4683320	0.84[EUR][1000 genomes]
rs4683322	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55724164	0.85[ASN][1000 genomes]
rs55927279	0.89[ASN][1000 genomes]
rs56217494	0.87[ASN][1000 genomes]
rs56249396	0.90[ASN][1000 genomes]
rs57756484	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58956475	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62246398	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62246451	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62246455	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6414435	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414436	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442055	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442059	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442060	0.85[ASN][1000 genomes]
rs6766230	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6767218	0.91[ASN][1000 genomes]
rs6767907	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768722	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6772670	0.85[EUR][1000 genomes]
rs6773521	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6777145	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6781941	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6785790	0.82[EUR][1000 genomes]
rs6791062	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7373821	0.83[ASN][1000 genomes]
rs7433300	0.94[ASN][1000 genomes]
rs749511	0.85[ASN][1000 genomes]
rs749512	0.85[ASN][1000 genomes]
rs7610620	0.91[ASN][1000 genomes]
rs7615323	0.81[EUR][1000 genomes]
rs7620997	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7623888	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7633435	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9311403	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812878	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818382	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9821119	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837343	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9843075	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9844122	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9845728	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9854790	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9858443	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875235	0.81[EUR][1000 genomes];0.94[ASN][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
rs11923706	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs11923706	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47126800-47168200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr3:47139600-47161800	Weak transcription	Fetal Brain Female	brain
3	chr3:47139800-47163200	Weak transcription	A549	lung
4	chr3:47140000-47175600	Weak transcription	Small Intestine	intestine
5	chr3:47144200-47170800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:47145800-47175000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:47146400-47164600	Weak transcription	Psoas Muscle	Psoas
8	chr3:47150800-47161400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:47150800-47166600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr3:47151200-47164400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:47151200-47164400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:47151200-47167400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:47151400-47161600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:47152400-47166000	Strong transcription	Placenta	Placenta
15	chr3:47154000-47164600	Weak transcription	Pancreas	Pancrea
16	chr3:47155200-47164600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:47155200-47165400	Weak transcription	Fetal Brain Male	brain
18	chr3:47155200-47172600	Weak transcription	Colonic Mucosa	Colon
19	chr3:47155400-47161600	Weak transcription	Aorta	Aorta
20	chr3:47155400-47162200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:47155400-47164400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:47155400-47164600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:47155400-47164600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:47155400-47164600	Weak transcription	Gastric	stomach
25	chr3:47155400-47164600	Weak transcription	Ovary	ovary
26	chr3:47155400-47165400	Weak transcription	Spleen	Spleen
27	chr3:47155400-47183800	Weak transcription	Esophagus	oesophagus
28	chr3:47155600-47161600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:47155600-47161600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:47155600-47162000	Weak transcription	Thymus	Thymus
31	chr3:47155600-47164200	Weak transcription	Lung	lung
32	chr3:47155600-47164400	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:47155800-47163400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:47155800-47163600	Weak transcription	Fetal Heart	heart
35	chr3:47155800-47164600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:47156000-47164600	Weak transcription	NHLF	lung
37	chr3:47156000-47164800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:47156000-47165000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:47156200-47165400	Weak transcription	Left Ventricle	heart
40	chr3:47156600-47161800	Strong transcription	GM12878-XiMat	blood
41	chr3:47156800-47164200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:47156800-47164800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:47157000-47161600	Weak transcription	HSMMtube	muscle
44	chr3:47157000-47162000	Weak transcription	Fetal Kidney	kidney
45	chr3:47157000-47162000	Weak transcription	Fetal Lung	lung
46	chr3:47157000-47164400	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:47157400-47162000	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:47157400-47162200	Weak transcription	HMEC	breast
49	chr3:47157400-47164600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:47157400-47165400	Weak transcription	Right Ventricle	heart

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