Variant report

Variant	rs12538769
Chromosome Location	chr7:106984288-106984289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 163 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs1002935	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs1018946	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs1018947	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs10253172	0.84[CEU][hapmap];0.82[YRI][hapmap]
rs10253291	0.84[CEU][hapmap]
rs10464620	0.94[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs10487271	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10953530	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs10953531	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs10953533	0.81[EUR][1000 genomes]
rs10953534	0.87[EUR][1000 genomes]
rs10953535	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10953536	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953537	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1121312	0.87[EUR][1000 genomes]
rs11761181	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11764448	0.87[EUR][1000 genomes]
rs11766131	0.85[EUR][1000 genomes]
rs11769527	0.87[EUR][1000 genomes]
rs11769861	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11769901	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11770061	0.85[EUR][1000 genomes]
rs11773514	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12154285	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12155231	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531187	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12532447	1.00[CEU][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12532514	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532849	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12532953	0.82[EUR][1000 genomes]
rs12532967	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12533516	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12533767	0.82[EUR][1000 genomes]
rs12534000	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12534676	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12535081	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535093	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535814	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12536485	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12536491	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12536603	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12537011	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12537374	0.84[EUR][1000 genomes]
rs12537730	0.81[EUR][1000 genomes]
rs12537733	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12537785	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538090	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540475	0.83[EUR][1000 genomes]
rs12705405	0.81[CEU][hapmap]
rs12705406	1.00[ASN][1000 genomes]
rs1548523	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1548524	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17349904	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs17350182	0.85[EUR][1000 genomes]
rs17403088	0.81[CEU][hapmap]
rs17427123	0.81[EUR][1000 genomes]
rs17427849	0.82[EUR][1000 genomes]
rs17428071	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17428126	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs17429118	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17429146	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17429825	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481842	0.84[CEU][hapmap]
rs1981696	0.84[CEU][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs1989814	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2023892	0.82[EUR][1000 genomes]
rs2107318	0.82[EUR][1000 genomes]
rs2107319	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2189501	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2249043	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2299422	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2395859	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2395880	0.85[EUR][1000 genomes]
rs2395881	0.85[EUR][1000 genomes]
rs257375	0.96[GIH][hapmap];0.87[TSI][hapmap]
rs257377	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs257378	0.84[CEU][hapmap]
rs257387	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs2894459	1.00[CEU][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3729876	0.84[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs3729877	0.84[CEU][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs3757713	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3779498	0.87[EUR][1000 genomes]
rs3779500	0.84[CEU][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs3801958	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3801959	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3801963	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3801965	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3815148	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3823959	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3823960	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4515482	0.84[EUR][1000 genomes]
rs4727670	0.82[EUR][1000 genomes]
rs4727671	0.84[EUR][1000 genomes]
rs4730223	1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs4730224	0.80[EUR][1000 genomes]
rs4730226	0.84[EUR][1000 genomes]
rs4730227	0.85[EUR][1000 genomes]
rs4730228	0.86[EUR][1000 genomes]
rs4730229	0.86[EUR][1000 genomes]
rs4730231	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4730232	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4730233	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730239	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730241	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730242	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730248	0.94[CEU][hapmap]
rs5002976	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57525841	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58319984	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58663672	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58689670	0.80[EUR][1000 genomes]
rs59782202	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59900773	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60255281	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61406169	0.85[EUR][1000 genomes]
rs61511581	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61673847	0.83[EUR][1000 genomes]
rs6466160	0.84[CEU][hapmap]
rs6466162	0.85[EUR][1000 genomes]
rs6946036	0.95[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs6946931	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs6947675	1.00[CEU][hapmap]
rs6947857	0.84[CEU][hapmap];0.82[YRI][hapmap]
rs6949961	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs6960148	0.84[CEU][hapmap];0.82[YRI][hapmap]
rs6960813	0.87[EUR][1000 genomes]
rs6963917	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6964798	0.87[EUR][1000 genomes]
rs6964966	0.87[EUR][1000 genomes]
rs6965001	0.87[EUR][1000 genomes]
rs6967639	0.81[EUR][1000 genomes]
rs6967745	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6971675	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6971774	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[EUR][1000 genomes]
rs6977868	0.81[CEU][hapmap]
rs7777976	0.84[EUR][1000 genomes]
rs7779062	0.84[EUR][1000 genomes]
rs7781947	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7783181	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7793594	0.84[EUR][1000 genomes]
rs7794598	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs7794915	0.89[GIH][hapmap];1.00[MEX][hapmap]
rs7794965	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs7798223	0.82[EUR][1000 genomes]
rs7800443	0.87[EUR][1000 genomes]
rs7803290	0.87[EUR][1000 genomes]
rs7804979	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807648	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809508	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810216	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs8180747	0.83[CEU][hapmap]
rs9641378	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs997311	0.91[AMR][1000 genomes];0.98[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	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	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12538769	LHFPL3	cis	parietal	SCAN
rs12538769	ATXN7L1	cis	parietal	SCAN
rs12538769	GPR22	cis	multi-tissue	Pritchard
rs12538769	NRCAM	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106888800-106999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:106923800-106999400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:106946200-106999800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:106946400-106999400	Weak transcription	Pancreas	Pancrea
5	chr7:106953800-106999400	Weak transcription	Left Ventricle	heart
6	chr7:106965400-106998000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:106967800-106999800	Weak transcription	Fetal Heart	heart
8	chr7:106973800-106996000	Weak transcription	Primary T cells from cord blood	blood
9	chr7:106973800-106998200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr7:106974000-106998000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr7:106974600-106999400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:106979200-106984400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:106982400-106999800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:106982800-106988000	Weak transcription	Fetal Kidney	kidney
15	chr7:106983400-106984800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr7:106983400-106985200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:106983600-106984800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr7:106983600-106985200	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr7:106984000-106999800	Weak transcription	Aorta	Aorta
20	chr7:106984200-106984600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:106984200-106984600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
22	chr7:106984200-106984800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:106984200-106984800	Strong transcription	Primary B cells from cord blood	blood
24	chr7:106984200-106985600	Strong transcription	Dnd41	blood
25	chr7:106984200-106996000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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