Variant report

Variant	rs12491473
Chromosome Location	chr3:46989904-46989905
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 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	chr3:46988418..46991129-chr3:46992863..46994642,3	MCF-7	breast:
4	chr3:46984582..46987726-chr3:46988178..46990594,3	K562	blood:
5	chr3:46988825..46991481-chr3:46997444..47000413,2	MCF-7	breast:
6	chr3:46989186..46991293-chr3:47035849..47039529,3	K562	blood:
7	chr3:46987488..46994423-chr3:47016253..47019914,6	MCF-7	breast:
8	chr3:46989810..46990729-chr4:6695069..6695746,2	Hela-S3	cervix:
9	chr3:46986886..46990722-chr3:47020544..47025137,5	MCF-7	breast:
10	chr3:46989415..46991130-chr3:47009222..47011268,2	MCF-7	breast:
11	chr3:46979992..46983614-chr3:46988969..46991376,3	MCF-7	breast:
12	chr3:46988383..46991103-chr3:47025292..47027507,2	MCF-7	breast:
13	chr3:46983747..46991522-chr3:47014474..47023916,13	MCF-7	breast:
14	chr3:46987136..46991583-chr3:47027983..47031367,6	K562	blood:
15	chr3:46968433..46974874-chr3:46985986..46991697,10	MCF-7	breast:
16	chr3:46983771..46985594-chr3:46988811..46991272,2	MCF-7	breast:
17	chr3:46987457..46990723-chr3:46999774..47002993,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction
ENSG00000163993	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10433549	0.84[EUR][1000 genomes]
rs10461018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1079276	0.93[EUR][1000 genomes]
rs1108301	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11130110	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130111	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130112	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11716553	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11720139	0.85[EUR][1000 genomes]
rs11917361	0.80[EUR][1000 genomes]
rs11917474	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12152493	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12630534	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13062681	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13066214	0.93[EUR][1000 genomes]
rs13077398	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13091054	0.84[EUR][1000 genomes]
rs1463393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17784127	0.82[EUR][1000 genomes]
rs1869869	0.96[EUR][1000 genomes]
rs1869871	0.88[EUR][1000 genomes]
rs2061197	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278963	0.85[EUR][1000 genomes]
rs2305634	0.93[EUR][1000 genomes]
rs2305635	0.85[EUR][1000 genomes]
rs2305638	0.88[EUR][1000 genomes]
rs2385867	0.89[EUR][1000 genomes]
rs34103310	0.86[EUR][1000 genomes]
rs34344887	0.92[EUR][1000 genomes]
rs4078466	0.82[EUR][1000 genomes]
rs4082155	0.82[EUR][1000 genomes]
rs4234465	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4682831	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4682837	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682844	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683296	0.81[AFR][1000 genomes]
rs55843455	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56217494	0.82[EUR][1000 genomes]
rs61729713	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62246375	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62246398	0.80[EUR][1000 genomes]
rs62248439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66539935	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66564457	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6763236	0.85[EUR][1000 genomes]
rs6774733	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6794193	0.84[EUR][1000 genomes]
rs6808742	0.88[EUR][1000 genomes]
rs749511	0.85[EUR][1000 genomes]
rs7610636	0.88[EUR][1000 genomes]
rs7617689	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7623898	0.81[AFR][1000 genomes]
rs7625067	0.86[EUR][1000 genomes]
rs7625070	0.86[EUR][1000 genomes]
rs7628747	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7633698	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7636252	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7637302	0.83[EUR][1000 genomes]
rs7640397	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7645278	0.81[AFR][1000 genomes]
rs9852082	0.81[AFR][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
rs12491473	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs12491473	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46976200-46990200	Weak transcription	Fetal Brain Male	brain
2	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:46978000-46990600	Strong transcription	Fetal Stomach	stomach
4	chr3:46979600-46994600	Genic enhancers	Fetal Thymus	thymus
5	chr3:46980200-46990800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:46982800-46992600	Enhancers	Left Ventricle	heart
7	chr3:46983000-46992600	Enhancers	Small Intestine	intestine
8	chr3:46983200-46992400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr3:46983400-46991200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:46983600-46992600	Enhancers	Psoas Muscle	Psoas
11	chr3:46983600-46992600	Enhancers	Right Atrium	heart
12	chr3:46983600-46994000	Enhancers	HUVEC	blood vessel
13	chr3:46984200-46996400	Enhancers	Liver	Liver
14	chr3:46985000-46992000	Enhancers	Pancreas	Pancrea
15	chr3:46985000-46992600	Enhancers	Right Ventricle	heart
16	chr3:46985200-46991800	Genic enhancers	Fetal Intestine Small	intestine
17	chr3:46985600-46995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:46985800-46990000	Genic enhancers	Primary B cells from peripheral blood	blood
19	chr3:46985800-46990800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:46985800-46994200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr3:46986000-46990800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:46986000-46991000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:46986200-46991000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:46986400-46991200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr3:46986600-46990600	Genic enhancers	GM12878-XiMat	blood
27	chr3:46986600-46990800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:46986600-46990800	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr3:46986600-46991000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:46986800-46990200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:46986800-46990800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:46986800-46992600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr3:46987000-46990000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:46987000-46990800	Weak transcription	Brain Angular Gyrus	brain
35	chr3:46987200-46990000	Genic enhancers	Spleen	Spleen
36	chr3:46987400-46990000	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr3:46987600-46990000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:46987600-46994800	Enhancers	Fetal Intestine Large	intestine
39	chr3:46988000-46990200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:46988000-46990200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
41	chr3:46988000-46990800	Genic enhancers	Fetal Muscle Trunk	muscle
42	chr3:46988000-46991400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:46988000-46991400	Flanking Active TSS	Hela-S3	cervix
44	chr3:46988000-46991800	Enhancers	Colon Smooth Muscle	Colon
45	chr3:46988000-46992400	Enhancers	Fetal Heart	heart
46	chr3:46988000-46992600	Enhancers	Placenta	Placenta
47	chr3:46988000-46994200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr3:46988000-47003200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr3:46988200-46990000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:46988200-46990200	Enhancers	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links