Variant report

Variant	rs9854790
Chromosome Location	chr3:47101306-47101307
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47099343..47101567-chr3:47110019..47111796,2	K562	blood:

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10433549	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1079276	0.83[EUR][1000 genomes]
rs1108301	0.81[EUR][1000 genomes]
rs11130111	0.81[EUR][1000 genomes]
rs11130112	0.81[EUR][1000 genomes]
rs11130114	0.80[EUR][1000 genomes]
rs11130115	0.80[EUR][1000 genomes]
rs11130126	0.81[AFR][1000 genomes]
rs11707736	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11708451	0.80[EUR][1000 genomes]
rs11709660	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11712716	0.80[EUR][1000 genomes]
rs11713693	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714373	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715121	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11716539	0.80[EUR][1000 genomes]
rs11719738	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11720139	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11915074	0.81[AFR][1000 genomes]
rs11917361	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11917474	0.81[EUR][1000 genomes]
rs11920354	0.86[AFR][1000 genomes]
rs11921117	0.83[AFR][1000 genomes]
rs11923706	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11925560	0.82[AFR][1000 genomes]
rs12493425	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12629262	0.80[EUR][1000 genomes]
rs12631730	0.86[ASN][1000 genomes]
rs12715421	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13061071	0.83[EUR][1000 genomes]
rs13062022	0.80[EUR][1000 genomes]
rs13062681	0.85[EUR][1000 genomes]
rs13066214	0.82[EUR][1000 genomes]
rs13077398	0.81[EUR][1000 genomes]
rs13084117	0.80[EUR][1000 genomes]
rs13091054	0.89[EUR][1000 genomes]
rs13098228	0.83[EUR][1000 genomes]
rs1466740	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1466741	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17784127	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1811652	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1869869	0.81[EUR][1000 genomes]
rs2088135	0.84[AFR][1000 genomes]
rs2278963	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305634	0.83[EUR][1000 genomes]
rs2305635	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305638	0.80[EUR][1000 genomes]
rs2385867	0.84[EUR][1000 genomes]
rs34103310	0.89[EUR][1000 genomes]
rs34344887	0.82[EUR][1000 genomes]
rs4018905	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4078466	0.87[EUR][1000 genomes]
rs4082155	0.88[EUR][1000 genomes]
rs4234465	0.81[EUR][1000 genomes]
rs4682831	0.81[EUR][1000 genomes]
rs4682852	0.80[EUR][1000 genomes]
rs4683322	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55724164	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55843455	0.81[EUR][1000 genomes]
rs55927279	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56217494	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56249396	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56250009	0.84[AFR][1000 genomes]
rs57756484	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58956475	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61729713	0.81[EUR][1000 genomes]
rs62246375	0.81[EUR][1000 genomes]
rs62246398	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62246402	0.88[AFR][1000 genomes]
rs62246451	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62246455	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62248905	0.88[AFR][1000 genomes]
rs6414435	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414436	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442059	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442060	0.84[ASN][1000 genomes]
rs66539935	0.81[EUR][1000 genomes]
rs6763236	0.91[EUR][1000 genomes]
rs6766230	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6767218	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6767907	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6768221	0.81[AFR][1000 genomes]
rs6768722	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6772670	0.80[EUR][1000 genomes]
rs6773521	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6777145	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6781941	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6785790	0.81[EUR][1000 genomes]
rs6791062	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794193	0.90[EUR][1000 genomes]
rs73069104	0.84[AFR][1000 genomes]
rs7373821	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7426969	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7433300	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs749511	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs749512	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7610620	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610636	0.85[EUR][1000 genomes]
rs7620997	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7621911	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7623888	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7625067	0.91[EUR][1000 genomes]
rs7625070	0.91[EUR][1000 genomes]
rs7632501	0.88[AFR][1000 genomes]
rs7633435	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633698	0.81[EUR][1000 genomes]
rs7636252	0.81[EUR][1000 genomes]
rs7637302	0.84[EUR][1000 genomes]
rs9311403	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9812878	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9818382	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9821119	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837343	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843075	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9844122	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9845728	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858443	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9875235	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9854790	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs9854790	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47078000-47130600	Weak transcription	Stomach Mucosa	stomach
2	chr3:47078800-47101400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:47079600-47123800	Weak transcription	Pancreas	Pancrea
4	chr3:47079600-47124200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:47079800-47124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:47083000-47106400	Weak transcription	Colonic Mucosa	Colon
7	chr3:47083200-47135200	Weak transcription	Small Intestine	intestine
8	chr3:47083400-47117200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:47083400-47138600	Weak transcription	Psoas Muscle	Psoas
10	chr3:47084200-47102800	Weak transcription	HUVEC	blood vessel
11	chr3:47084400-47104800	Weak transcription	Fetal Kidney	kidney
12	chr3:47084400-47116000	Weak transcription	Right Ventricle	heart
13	chr3:47088200-47112800	Weak transcription	NHDF-Ad	bronchial
14	chr3:47089000-47117000	Weak transcription	Fetal Heart	heart
15	chr3:47089400-47107000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:47089600-47103600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:47093400-47122600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:47093600-47109800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:47093800-47123400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:47094200-47123800	Weak transcription	Esophagus	oesophagus
21	chr3:47094600-47113400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:47095800-47121000	Weak transcription	Fetal Brain Male	brain
23	chr3:47096200-47111200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:47096800-47105400	Strong transcription	Fetal Intestine Small	intestine
25	chr3:47096800-47108200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:47097600-47108800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:47097800-47105400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr3:47098800-47101400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:47098800-47101600	Weak transcription	Hela-S3	cervix
30	chr3:47098800-47103000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:47098800-47103600	Weak transcription	Fetal Lung	lung
32	chr3:47098800-47104400	Weak transcription	GM12878-XiMat	blood
33	chr3:47098800-47105600	Weak transcription	NH-A	brain
34	chr3:47098800-47106600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:47098800-47106600	Weak transcription	Ovary	ovary
36	chr3:47098800-47115200	Weak transcription	HSMMtube	muscle
37	chr3:47098800-47118200	Weak transcription	NHLF	lung
38	chr3:47098800-47121800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:47098800-47122000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:47098800-47122000	Weak transcription	Aorta	Aorta
41	chr3:47098800-47149600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:47099000-47101400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:47099000-47101600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:47099000-47101600	Weak transcription	Fetal Intestine Large	intestine
45	chr3:47099000-47101600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:47099000-47102200	Weak transcription	HSMM	muscle
47	chr3:47099000-47102800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:47099000-47102800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr3:47099000-47103000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:47099000-47103400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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