Variant report

Variant	rs7426969
Chromosome Location	chr3:47091355-47091356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10433549	0.80[EUR][1000 genomes]
rs11707736	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11709660	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11715121	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11720139	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11917361	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12715421	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17784127	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2278963	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2305635	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4018905	0.82[EUR][1000 genomes]
rs4683322	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55724164	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55927279	0.85[AMR][1000 genomes]
rs56217494	0.83[AMR][1000 genomes]
rs56249396	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62246398	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6414435	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6414436	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442055	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6763236	0.80[EUR][1000 genomes]
rs6767218	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6768722	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6777145	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7373821	0.80[EUR][1000 genomes]
rs7433300	0.81[ASN][1000 genomes]
rs749511	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7610620	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7625067	0.81[EUR][1000 genomes]
rs7625070	0.81[EUR][1000 genomes]
rs7633435	0.85[EUR][1000 genomes]
rs9311403	0.81[EUR][1000 genomes]
rs9844122	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9845728	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9854790	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9858443	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9875235	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	esv3397719	chr3:47090398-47092646	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3389796	chr3:47091278-47091453	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7426969	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs7426969	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr3:47079400-47095800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:47079600-47123800	Weak transcription	Pancreas	Pancrea
5	chr3:47079600-47124200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:47079800-47095000	Weak transcription	HMEC	breast
7	chr3:47079800-47098000	Weak transcription	Aorta	Aorta
8	chr3:47079800-47124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:47080000-47095200	Weak transcription	Fetal Brain Male	brain
10	chr3:47083000-47098000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:47083000-47098000	Weak transcription	A549	lung
12	chr3:47083000-47098400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:47083000-47106400	Weak transcription	Colonic Mucosa	Colon
14	chr3:47083200-47097800	Weak transcription	Gastric	stomach
15	chr3:47083200-47098000	Weak transcription	Brain Germinal Matrix	brain
16	chr3:47083200-47098000	Weak transcription	Ovary	ovary
17	chr3:47083200-47098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:47083200-47135200	Weak transcription	Small Intestine	intestine
19	chr3:47083400-47117200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:47083400-47138600	Weak transcription	Psoas Muscle	Psoas
21	chr3:47083800-47097600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:47083800-47097600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:47083800-47097800	Weak transcription	Fetal Brain Female	brain
24	chr3:47083800-47098000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:47083800-47098200	Weak transcription	NHLF	lung
26	chr3:47084000-47098000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:47084200-47093800	Weak transcription	Esophagus	oesophagus
28	chr3:47084200-47094600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:47084200-47097800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:47084200-47097800	Weak transcription	Spleen	Spleen
31	chr3:47084200-47098000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:47084200-47098000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:47084200-47098200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:47084200-47098200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:47084200-47098200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:47084200-47098200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:47084200-47098400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:47084200-47102800	Weak transcription	HUVEC	blood vessel
39	chr3:47084400-47097800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:47084400-47104800	Weak transcription	Fetal Kidney	kidney
41	chr3:47084400-47116000	Weak transcription	Right Ventricle	heart
42	chr3:47084800-47097800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:47084800-47098000	Weak transcription	Fetal Lung	lung
44	chr3:47085200-47095000	Weak transcription	Osteobl	bone
45	chr3:47085400-47094800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:47086400-47095200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:47086600-47093400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr3:47086600-47093400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:47086600-47094600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:47086600-47094800	Weak transcription	HepG2	liver

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