Variant report

Variant	rs6774733
Chromosome Location	chr3:46991241-46991242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46988980..46994216-chr3:47016439..47022535,7	K562	blood:
2	chr3:46988617..46992704-chr3:46994196..46998366,6	K562	blood:
3	chr3:46988825..46991481-chr3:46997444..47000413,2	MCF-7	breast:
4	chr3:46989186..46991293-chr3:47035849..47039529,3	K562	blood:
5	chr3:46987488..46994423-chr3:47016253..47019914,6	MCF-7	breast:
6	chr3:46979992..46983614-chr3:46988969..46991376,3	MCF-7	breast:
7	chr3:46983747..46991522-chr3:47014474..47023916,13	MCF-7	breast:
8	chr3:46990736..46992416-chr3:47023933..47026692,2	K562	blood:
9	chr3:46987136..46991583-chr3:47027983..47031367,6	K562	blood:
10	chr3:46968433..46974874-chr3:46985986..46991697,10	MCF-7	breast:
11	chr3:46983771..46985594-chr3:46988811..46991272,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160796	Chromatin interaction
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10433549	0.84[EUR][1000 genomes]
rs10461018	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1079276	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1108301	0.96[EUR][1000 genomes]
rs11130110	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130111	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130112	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11716553	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11720139	0.84[EUR][1000 genomes]
rs11917474	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12152493	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12491473	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12630534	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13062681	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13066214	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13077398	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13091054	0.84[EUR][1000 genomes]
rs1463393	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17784127	0.81[EUR][1000 genomes]
rs1869869	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1869871	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2061197	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278963	0.85[EUR][1000 genomes]
rs2305634	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2305635	0.85[EUR][1000 genomes]
rs2305638	0.89[EUR][1000 genomes]
rs2385867	0.90[EUR][1000 genomes]
rs34103310	0.86[EUR][1000 genomes]
rs34344887	0.93[EUR][1000 genomes]
rs4078466	0.82[EUR][1000 genomes]
rs4082155	0.83[EUR][1000 genomes]
rs4234465	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682831	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682837	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682844	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55843455	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56217494	0.81[EUR][1000 genomes]
rs61729713	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62246375	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62248439	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66539935	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66564457	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6763236	0.86[EUR][1000 genomes]
rs6794193	0.85[EUR][1000 genomes]
rs6808742	0.88[EUR][1000 genomes]
rs749511	0.85[EUR][1000 genomes]
rs7610636	0.89[EUR][1000 genomes]
rs7617689	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7625067	0.86[EUR][1000 genomes]
rs7625070	0.86[EUR][1000 genomes]
rs7628747	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633698	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7636252	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7637302	0.83[EUR][1000 genomes]
rs7640397	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6774733	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs6774733	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	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:46979600-46994600	Genic enhancers	Fetal Thymus	thymus
3	chr3:46982800-46992600	Enhancers	Left Ventricle	heart
4	chr3:46983000-46992600	Enhancers	Small Intestine	intestine
5	chr3:46983200-46992400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:46983600-46992600	Enhancers	Psoas Muscle	Psoas
7	chr3:46983600-46992600	Enhancers	Right Atrium	heart
8	chr3:46983600-46994000	Enhancers	HUVEC	blood vessel
9	chr3:46984200-46996400	Enhancers	Liver	Liver
10	chr3:46985000-46992000	Enhancers	Pancreas	Pancrea
11	chr3:46985000-46992600	Enhancers	Right Ventricle	heart
12	chr3:46985200-46991800	Genic enhancers	Fetal Intestine Small	intestine
13	chr3:46985600-46995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:46985800-46994200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:46986800-46992600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr3:46987600-46994800	Enhancers	Fetal Intestine Large	intestine
18	chr3:46988000-46991400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:46988000-46991400	Flanking Active TSS	Hela-S3	cervix
20	chr3:46988000-46991800	Enhancers	Colon Smooth Muscle	Colon
21	chr3:46988000-46992400	Enhancers	Fetal Heart	heart
22	chr3:46988000-46992600	Enhancers	Placenta	Placenta
23	chr3:46988000-46994200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:46988000-47003200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr3:46988200-46992000	Genic enhancers	Fetal Muscle Leg	muscle
26	chr3:46988200-46992600	Enhancers	Lung	lung
27	chr3:46988400-46991800	Enhancers	Brain Hippocampus Middle	brain
28	chr3:46988400-46994600	Genic enhancers	Dnd41	blood
29	chr3:46988600-46991400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:46988600-46994400	Enhancers	Primary hematopoietic stem cells	blood
31	chr3:46989000-46992600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr3:46989200-46992000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:46989200-46992000	Enhancers	Esophagus	oesophagus
34	chr3:46989200-46992600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:46989200-46995400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:46989600-46991800	Enhancers	NHEK	skin
37	chr3:46989600-46992800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:46989600-46993200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr3:46989800-46991800	Enhancers	Brain Anterior Caudate	brain
40	chr3:46989800-46992000	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr3:46989800-46992200	Enhancers	Stomach Mucosa	stomach
42	chr3:46989800-46992800	Enhancers	Primary B cells from cord blood	blood
43	chr3:46989800-46992800	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr3:46989800-46993200	Enhancers	Adipose Nuclei	Adipose
45	chr3:46989800-46993800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:46989800-46995200	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr3:46989800-46998600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:46989800-47000600	Weak transcription	Brain Germinal Matrix	brain
49	chr3:46989800-47000600	Weak transcription	NHDF-Ad	bronchial
50	chr3:46989800-47001200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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