Variant report

Variant	rs6794193
Chromosome Location	chr3:47114904-47114905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47097362..47099843-chr3:47113301..47116271,2	K562	blood:
2	chr3:47113958..47116821-chr3:47117778..47119607,2	K562	blood:
3	chr3:47114506..47116285-chr3:47366485..47368143,2	K562	blood:

Extended variants
information (count: 146 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10433549	0.91[CEU][hapmap]
rs10461018	0.96[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs1079276	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1108301	0.87[EUR][1000 genomes]
rs11130110	0.93[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs11130111	0.96[CEU][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs11130112	0.96[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs11130114	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130123	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]
rs11130124	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap]
rs11130126	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs11707736	0.84[EUR][1000 genomes]
rs11708451	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11709660	0.87[EUR][1000 genomes]
rs11710013	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs11712716	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11714282	0.80[ASN][1000 genomes]
rs11715121	0.87[EUR][1000 genomes]
rs11716539	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11716553	0.82[EUR][1000 genomes]
rs11718795	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11719306	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11719738	0.80[EUR][1000 genomes]
rs11719795	0.81[JPT][hapmap]
rs11720139	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11915074	0.82[CEU][hapmap]
rs11917361	0.88[EUR][1000 genomes]
rs11917474	0.88[EUR][1000 genomes]
rs11920853	0.82[CEU][hapmap]
rs12152493	0.86[EUR][1000 genomes]
rs12488225	0.82[EUR][1000 genomes]
rs12489211	0.85[EUR][1000 genomes]
rs12491473	0.84[EUR][1000 genomes]
rs12493425	0.80[EUR][1000 genomes]
rs12629262	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12630534	0.84[EUR][1000 genomes]
rs12635619	0.83[EUR][1000 genomes]
rs12715421	0.89[EUR][1000 genomes]
rs13061071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13062022	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13062681	0.82[EUR][1000 genomes]
rs13066214	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13077398	0.88[EUR][1000 genomes]
rs13084117	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13087426	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13091054	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094438	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap]
rs13094672	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13098228	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1463393	0.84[EUR][1000 genomes]
rs1466741	0.88[CEU][hapmap]
rs17784127	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1811652	0.80[EUR][1000 genomes]
rs1869869	0.88[EUR][1000 genomes]
rs2061197	0.96[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2132173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2276853	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs2276854	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs2278963	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2290546	0.81[JPT][hapmap]
rs2305634	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305635	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2305638	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2385867	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34103310	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34344887	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4018905	0.84[EUR][1000 genomes]
rs4078466	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4082155	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234465	0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs4587	0.81[JPT][hapmap]
rs4682831	0.87[EUR][1000 genomes]
rs4682837	0.96[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs4682844	0.96[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4682852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683297	0.81[JPT][hapmap]
rs4683298	0.81[JPT][hapmap]
rs4683301	0.81[YRI][hapmap]
rs4683320	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683322	0.92[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs4683326	0.88[CEU][hapmap]
rs55724164	0.82[EUR][1000 genomes]
rs55843455	0.86[EUR][1000 genomes]
rs56249396	0.85[EUR][1000 genomes]
rs61729713	0.87[EUR][1000 genomes]
rs62246375	0.87[EUR][1000 genomes]
rs62246398	0.85[EUR][1000 genomes]
rs62246451	0.80[EUR][1000 genomes]
rs62248439	0.84[EUR][1000 genomes]
rs6414435	0.89[EUR][1000 genomes]
rs6414436	0.85[EUR][1000 genomes]
rs6442040	0.81[JPT][hapmap]
rs6442055	0.90[EUR][1000 genomes]
rs6442059	0.80[EUR][1000 genomes]
rs66539935	0.87[EUR][1000 genomes]
rs66564457	0.87[EUR][1000 genomes]
rs6763236	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766230	0.80[EUR][1000 genomes]
rs6767218	0.85[EUR][1000 genomes]
rs6767907	0.92[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs6768221	0.81[CEU][hapmap]
rs6768722	0.87[EUR][1000 genomes]
rs6772670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6774733	0.85[EUR][1000 genomes]
rs6777145	0.90[EUR][1000 genomes]
rs6785790	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6791842	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap]
rs6808742	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs724448	0.81[YRI][hapmap]
rs724449	0.81[YRI][hapmap]
rs7373821	0.80[EUR][1000 genomes]
rs7433300	0.81[CEU][hapmap]
rs749511	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs749512	0.85[CEU][hapmap]
rs7610620	0.86[EUR][1000 genomes]
rs7610636	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7615323	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7617689	0.84[EUR][1000 genomes]
rs7621911	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7625067	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625070	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628747	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs7633435	0.87[EUR][1000 genomes]
rs7633698	0.88[EUR][1000 genomes]
rs7636252	0.88[EUR][1000 genomes]
rs7637302	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7640397	0.85[EUR][1000 genomes]
rs7645278	0.81[JPT][hapmap]
rs9311403	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs9818382	0.80[EUR][1000 genomes]
rs9821119	0.80[EUR][1000 genomes]
rs9837343	0.92[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs9844122	0.88[EUR][1000 genomes]
rs9845728	0.88[EUR][1000 genomes]
rs9852082	0.81[JPT][hapmap]
rs9854790	0.90[EUR][1000 genomes]
rs9855938	0.81[JPT][hapmap]
rs9858443	0.89[EUR][1000 genomes]
rs9875235	0.87[EUR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6794193	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs6794193	CCDC12	cis	cerebellum	SCAN
rs6794193	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs6794193	HYAL2	cis	cerebellum	SCAN
rs6794193	SCAP	cis	parietal	SCAN
rs6794193	C3orf75	cis	cerebellum	SCAN
rs6794193	PRKAR2A	cis	cerebellum	SCAN

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	chr3:47079600-47123800	Weak transcription	Pancreas	Pancrea
3	chr3:47079600-47124200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47079800-47124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:47083200-47135200	Weak transcription	Small Intestine	intestine
6	chr3:47083400-47117200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:47083400-47138600	Weak transcription	Psoas Muscle	Psoas
8	chr3:47084400-47116000	Weak transcription	Right Ventricle	heart
9	chr3:47089000-47117000	Weak transcription	Fetal Heart	heart
10	chr3:47093400-47122600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:47093800-47123400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:47094200-47123800	Weak transcription	Esophagus	oesophagus
13	chr3:47095800-47121000	Weak transcription	Fetal Brain Male	brain
14	chr3:47098800-47115200	Weak transcription	HSMMtube	muscle
15	chr3:47098800-47118200	Weak transcription	NHLF	lung
16	chr3:47098800-47121800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:47098800-47122000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:47098800-47122000	Weak transcription	Aorta	Aorta
19	chr3:47098800-47149600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:47099000-47115000	Weak transcription	Brain Angular Gyrus	brain
21	chr3:47099000-47118200	Weak transcription	Brain Anterior Caudate	brain
22	chr3:47099000-47121600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:47099000-47121800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:47099000-47121800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:47099000-47121800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:47099000-47122000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:47099000-47122000	Weak transcription	Gastric	stomach
28	chr3:47099000-47125200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:47099000-47128200	Weak transcription	Spleen	Spleen
30	chr3:47099200-47119200	Weak transcription	A549	lung
31	chr3:47099200-47122000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:47100000-47118000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:47100000-47122200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:47101000-47125200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:47101200-47123800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:47101400-47147800	Strong transcription	Dnd41	blood
37	chr3:47101600-47123800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:47101800-47121800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:47102200-47115800	Weak transcription	Hela-S3	cervix
40	chr3:47103800-47122000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:47104200-47117400	Weak transcription	HUVEC	blood vessel
42	chr3:47105000-47116600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:47105000-47121800	Weak transcription	HMEC	breast
44	chr3:47105200-47117000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:47105200-47118000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:47106000-47117200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:47106200-47121800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:47106800-47121600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:47106800-47121600	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:47107000-47121800	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links