Variant report

Variant	rs12537785
Chromosome Location	chr7:107050221-107050222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:107042056..107044075-chr7:107048262..107050371,2	K562	blood:

Extended variants
information (count: 118 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1018946	1.00[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs1018947	1.00[CEU][hapmap]
rs10464620	0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs10487271	1.00[CEU][hapmap]
rs10953534	0.81[EUR][1000 genomes]
rs10953535	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10953536	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953537	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1121312	0.81[EUR][1000 genomes]
rs11761181	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11764448	0.81[EUR][1000 genomes]
rs11766131	0.91[EUR][1000 genomes]
rs11769527	0.81[EUR][1000 genomes]
rs11769861	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11769901	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11770061	0.91[EUR][1000 genomes]
rs11773514	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12154285	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12155231	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531187	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12532447	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12532514	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532849	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12532967	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12533516	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12534000	0.91[EUR][1000 genomes]
rs12534676	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12535081	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535093	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535814	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12536485	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12536491	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12536603	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12537011	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12537733	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12538090	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538769	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538848	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539895	0.84[EUR][1000 genomes]
rs1548523	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1548524	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17349904	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs17403088	0.81[CEU][hapmap]
rs17428071	1.00[CEU][hapmap]
rs17428126	0.94[CEU][hapmap]
rs17429118	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17429146	0.91[EUR][1000 genomes]
rs17429825	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481842	0.84[CEU][hapmap]
rs1978085	0.83[EUR][1000 genomes]
rs1989814	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2107319	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs2189501	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2249043	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2299422	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2395859	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2395880	0.91[EUR][1000 genomes]
rs2395881	0.91[EUR][1000 genomes]
rs2894459	1.00[CEU][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34084719	0.83[EUR][1000 genomes]
rs3757713	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3779498	0.81[EUR][1000 genomes]
rs3801958	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3801959	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3801963	1.00[CEU][hapmap]
rs3815148	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3823959	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3823960	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4515482	0.90[EUR][1000 genomes]
rs4730228	0.80[EUR][1000 genomes]
rs4730229	0.80[EUR][1000 genomes]
rs4730231	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4730232	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4730233	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730239	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730241	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730242	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730248	0.94[CEU][hapmap]
rs4730250	0.85[GIH][hapmap];0.84[MEX][hapmap]
rs5002976	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57525841	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58319984	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58663672	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58689670	0.86[EUR][1000 genomes]
rs59782202	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59900773	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60255281	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61511581	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6946036	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap]
rs6949961	1.00[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs6960813	0.81[EUR][1000 genomes]
rs6963917	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6964798	0.81[EUR][1000 genomes]
rs6964966	0.81[EUR][1000 genomes]
rs6965001	0.81[EUR][1000 genomes]
rs6967745	1.00[CEU][hapmap]
rs6979368	0.84[EUR][1000 genomes]
rs763386	0.85[GIH][hapmap];0.84[MEX][hapmap]
rs7781947	1.00[CEU][hapmap]
rs7783181	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7800443	0.81[EUR][1000 genomes]
rs7803290	0.81[EUR][1000 genomes]
rs7804979	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807648	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809508	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810216	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180747	0.83[CEU][hapmap]
rs9641378	1.00[CEU][hapmap]
rs997311	0.87[AMR][1000 genomes];0.91[EUR][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	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv608073	chr7:106960515-107063686	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1019963	chr7:107033342-107188641	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv539052	chr7:107033342-107188641	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12537785	LHFPL3	cis	parietal	SCAN
rs12537785	GPR22	Cis_1M	lymphoblastoid	RTeQTL
rs12537785	COG5	cis	parietal	SCAN
rs12537785	NRCAM	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107001400-107053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:107022200-107053000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:107027400-107053400	Weak transcription	Gastric	stomach
4	chr7:107027800-107086800	Weak transcription	Aorta	Aorta
5	chr7:107028000-107052800	Weak transcription	Fetal Muscle Leg	muscle
6	chr7:107028000-107054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:107028200-107053000	Weak transcription	Fetal Stomach	stomach
8	chr7:107028200-107082400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:107028200-107103800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:107028800-107053000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:107028800-107053200	Weak transcription	K562	blood
12	chr7:107029400-107050400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:107031600-107069600	Weak transcription	Fetal Kidney	kidney
14	chr7:107032400-107068000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr7:107033800-107069800	Weak transcription	Small Intestine	intestine
16	chr7:107034000-107055600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:107035800-107052800	Weak transcription	HSMMtube	muscle
18	chr7:107035800-107133000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr7:107036000-107050800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:107036200-107051000	Weak transcription	Liver	Liver
21	chr7:107036800-107069800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr7:107037000-107053200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr7:107037000-107069800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr7:107037800-107102200	Weak transcription	Ovary	ovary
25	chr7:107038000-107054000	Weak transcription	Fetal Heart	heart
26	chr7:107038200-107069600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr7:107038800-107100600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr7:107039000-107050600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr7:107039000-107068000	Weak transcription	Lung	lung
30	chr7:107039200-107050600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:107040200-107051400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:107040200-107069800	Weak transcription	Fetal Intestine Small	intestine
33	chr7:107041000-107070000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr7:107041200-107053000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr7:107042400-107053800	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:107044400-107065200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr7:107044800-107053200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr7:107045200-107053000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr7:107045400-107053000	Weak transcription	HUVEC	blood vessel
40	chr7:107045800-107051600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr7:107046000-107051200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr7:107046000-107053800	Weak transcription	HepG2	liver
43	chr7:107046000-107054200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr7:107046400-107051200	Weak transcription	Left Ventricle	heart
45	chr7:107046400-107053800	Weak transcription	Brain Hippocampus Middle	brain
46	chr7:107046400-107054000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr7:107046400-107055200	Weak transcription	Pancreas	Pancrea
48	chr7:107046400-107081800	Weak transcription	HSMM	muscle
49	chr7:107046600-107053800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:107046600-107054000	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links