Variant report

Variant	rs56249396
Chromosome Location	chr3:47067396-47067397
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	chr3:47066773..47068763-chr3:47068912..47071428,2	K562	blood:

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10433549	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1079276	0.84[EUR][1000 genomes]
rs1108301	0.83[EUR][1000 genomes]
rs11130111	0.82[EUR][1000 genomes]
rs11130112	0.82[EUR][1000 genomes]
rs11707736	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11709660	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11713693	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714373	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715121	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719738	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11720139	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11917361	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11917474	0.82[EUR][1000 genomes]
rs11923706	0.90[ASN][1000 genomes]
rs12152493	0.81[EUR][1000 genomes]
rs12493425	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12631730	0.82[ASN][1000 genomes]
rs12715421	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13062681	0.87[EUR][1000 genomes]
rs13066214	0.84[EUR][1000 genomes]
rs13077398	0.82[EUR][1000 genomes]
rs13091054	0.84[EUR][1000 genomes]
rs1466740	0.83[ASN][1000 genomes]
rs1466741	0.83[ASN][1000 genomes]
rs17784127	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1811652	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1869869	0.82[EUR][1000 genomes]
rs2278963	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305634	0.84[EUR][1000 genomes]
rs2305635	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305638	0.83[EUR][1000 genomes]
rs2385867	0.87[EUR][1000 genomes]
rs34103310	0.89[EUR][1000 genomes]
rs34344887	0.83[EUR][1000 genomes]
rs4018905	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4078466	0.85[EUR][1000 genomes]
rs4082155	0.85[EUR][1000 genomes]
rs4234465	0.83[EUR][1000 genomes]
rs4682831	0.83[EUR][1000 genomes]
rs4683322	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55724164	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55843455	0.83[EUR][1000 genomes]
rs55927279	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56217494	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57756484	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs58956475	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61729713	0.83[EUR][1000 genomes]
rs62246375	0.82[EUR][1000 genomes]
rs62246398	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62246451	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62246455	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6414435	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414436	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442055	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442059	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6442060	0.81[ASN][1000 genomes]
rs66539935	0.83[EUR][1000 genomes]
rs66564457	0.81[EUR][1000 genomes]
rs6763236	0.87[EUR][1000 genomes]
rs6766230	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6767218	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767907	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6768722	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773521	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6777145	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6781941	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6791062	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6794193	0.85[EUR][1000 genomes]
rs6808742	0.81[EUR][1000 genomes]
rs7373821	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7426969	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7433300	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs749511	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs749512	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7610620	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7610636	0.88[EUR][1000 genomes]
rs7620997	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7621911	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7623888	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7625067	0.86[EUR][1000 genomes]
rs7625070	0.86[EUR][1000 genomes]
rs7633435	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7633698	0.82[EUR][1000 genomes]
rs7636252	0.82[EUR][1000 genomes]
rs7637302	0.85[EUR][1000 genomes]
rs9311403	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9812878	0.92[ASN][1000 genomes]
rs9818382	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9821119	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837343	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9844122	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9845728	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9854790	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9858443	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875235	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56249396	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs56249396	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	chr3:47058800-47069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:47059800-47073000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:47060600-47073800	Weak transcription	Lung	lung
4	chr3:47061000-47076200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:47061000-47079000	Weak transcription	Fetal Brain Male	brain
6	chr3:47061200-47069600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:47061200-47069800	Weak transcription	Spleen	Spleen
8	chr3:47061200-47072400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:47061200-47076000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:47061200-47083000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:47061400-47069600	Weak transcription	HMEC	breast
12	chr3:47061400-47073600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:47061400-47074600	Weak transcription	Hela-S3	cervix
14	chr3:47061400-47076000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:47061400-47076200	Weak transcription	HSMMtube	muscle
16	chr3:47061800-47069800	Weak transcription	Placenta	Placenta
17	chr3:47061800-47074200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:47061800-47074600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:47062000-47069600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:47062000-47069600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:47062000-47069600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:47062000-47070200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:47062000-47071800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:47062000-47075400	Weak transcription	A549	lung
25	chr3:47062200-47069600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:47062200-47069600	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:47062200-47070200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:47062200-47073400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:47062200-47073400	Weak transcription	GM12878-XiMat	blood
30	chr3:47062200-47075000	Weak transcription	Brain Germinal Matrix	brain
31	chr3:47062200-47075400	Weak transcription	Aorta	Aorta
32	chr3:47062200-47076000	Weak transcription	Fetal Kidney	kidney
33	chr3:47062200-47077800	Weak transcription	Colonic Mucosa	Colon
34	chr3:47062400-47068200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:47062400-47069600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:47062400-47069600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:47062400-47069600	Weak transcription	Fetal Intestine Large	intestine
38	chr3:47062400-47074800	Weak transcription	HUVEC	blood vessel
39	chr3:47062800-47069600	Weak transcription	Primary B cells from cord blood	blood
40	chr3:47062800-47072400	Weak transcription	HSMM	muscle
41	chr3:47062800-47075400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:47062800-47076400	Weak transcription	Fetal Brain Female	brain
43	chr3:47063000-47068000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:47063000-47069600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:47063200-47069600	Weak transcription	NHEK	skin
46	chr3:47063200-47079000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:47064000-47073800	Weak transcription	Thymus	Thymus
48	chr3:47064400-47069400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:47064400-47069600	Weak transcription	Left Ventricle	heart
50	chr3:47064400-47071000	Weak transcription	Fetal Lung	lung

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