Variant report

Variant	rs1796379
Chromosome Location	chr12:42793611-42793612
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1043652	0.96[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1043656	0.96[CEU][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880275	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs10880279	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs10880282	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880284	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181421	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181427	0.97[EUR][1000 genomes]
rs11181453	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181461	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[ASN][1000 genomes]
rs11181484	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229224	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12229266	0.96[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12230583	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12231335	0.90[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12422938	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12423383	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12425945	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12578312	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs1376931	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1629725	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669884	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs1669888	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1669890	0.97[EUR][1000 genomes]
rs1669891	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669894	0.99[EUR][1000 genomes]
rs1669895	0.99[EUR][1000 genomes]
rs1669897	0.99[EUR][1000 genomes]
rs1669898	0.99[EUR][1000 genomes]
rs1669899	0.97[EUR][1000 genomes]
rs1669900	0.99[EUR][1000 genomes]
rs1669901	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669903	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669905	0.99[EUR][1000 genomes]
rs1669911	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669912	0.99[EUR][1000 genomes]
rs1669913	0.99[EUR][1000 genomes]
rs1669914	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669935	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669937	0.92[CEU][hapmap];0.99[EUR][1000 genomes]
rs17091052	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1796354	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796355	0.99[EUR][1000 genomes]
rs1796356	0.99[EUR][1000 genomes]
rs1796357	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796359	0.98[EUR][1000 genomes]
rs1796360	0.98[EUR][1000 genomes]
rs1796365	0.99[EUR][1000 genomes]
rs1796373	0.99[EUR][1000 genomes]
rs1796374	0.99[EUR][1000 genomes]
rs1796377	0.99[EUR][1000 genomes]
rs1796385	0.99[EUR][1000 genomes]
rs1796387	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796389	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796395	0.95[EUR][1000 genomes]
rs1796396	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796397	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796398	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1961953	0.84[EUR][1000 genomes]
rs2053946	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2061191	0.82[EUR][1000 genomes]
rs2061192	0.81[EUR][1000 genomes]
rs2243465	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2406872	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406969	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2600911	0.99[EUR][1000 genomes]
rs2600912	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2600916	0.99[EUR][1000 genomes]
rs2600917	0.89[EUR][1000 genomes]
rs2600918	0.99[EUR][1000 genomes]
rs2708063	0.99[EUR][1000 genomes]
rs2708069	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708075	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708077	0.91[EUR][1000 genomes]
rs2708506	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952653	0.99[EUR][1000 genomes]
rs3213989	0.88[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs3747563	0.90[EUR][1000 genomes]
rs3761677	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3827524	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4603368	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768397	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768398	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768401	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768412	0.92[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6582392	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs712126	0.80[CEU][hapmap]
rs712129	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs7134895	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs721447	0.98[EUR][1000 genomes]
rs7298965	0.82[EUR][1000 genomes]
rs73122408	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73122414	0.98[EUR][1000 genomes]
rs73122418	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7486516	0.84[EUR][1000 genomes]
rs752767	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7956016	1.00[ASW][hapmap];0.80[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap]
rs7960176	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs7975518	0.80[CEU][hapmap]
rs896555	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs896556	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1796379	KIF21A	cis	parietal	SCAN
rs1796379	NELL2	cis	parietal	SCAN
rs1796379	CPNE8	cis	parietal	SCAN
rs1796379	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42721600-42800800	Weak transcription	Psoas Muscle	Psoas
3	chr12:42721600-42803600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:42721800-42797000	Weak transcription	NHLF	lung
5	chr12:42721800-42803600	Weak transcription	Gastric	stomach
6	chr12:42732200-42794400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:42733400-42796800	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:42738200-42823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:42763800-42804200	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:42766200-42796800	Weak transcription	Aorta	Aorta
11	chr12:42767200-42836200	Weak transcription	Esophagus	oesophagus
12	chr12:42769800-42794200	Weak transcription	Left Ventricle	heart
13	chr12:42770000-42794000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:42770200-42815800	Weak transcription	Fetal Lung	lung
15	chr12:42770400-42795400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:42770400-42816600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:42771000-42795000	Weak transcription	HSMMtube	muscle
18	chr12:42771000-42796800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:42771000-42799000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:42771200-42794400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:42771200-42801000	Weak transcription	NH-A	brain
22	chr12:42771800-42803000	Weak transcription	Brain Anterior Caudate	brain
23	chr12:42776200-42795400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:42777000-42802600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:42778000-42798200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:42779000-42798400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:42779400-42797800	Weak transcription	Brain Germinal Matrix	brain
28	chr12:42779800-42795000	Weak transcription	Osteobl	bone
29	chr12:42780200-42802800	Weak transcription	Right Ventricle	heart
30	chr12:42780200-42836000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:42780400-42794800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:42780400-42795000	Weak transcription	NHEK	skin
33	chr12:42780400-42804200	Weak transcription	K562	blood
34	chr12:42780400-42811200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:42782000-42802000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:42782800-42797000	Weak transcription	Ovary	ovary
37	chr12:42782800-42803400	Weak transcription	Spleen	Spleen
38	chr12:42782800-42804200	Weak transcription	Fetal Brain Female	brain
39	chr12:42782800-42807200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:42783000-42836000	Weak transcription	Lung	lung
41	chr12:42783200-42795200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:42784000-42794200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:42784000-42795200	Weak transcription	A549	lung
44	chr12:42784400-42794400	Weak transcription	Thymus	Thymus
45	chr12:42784400-42795000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr12:42785000-42794200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:42785200-42794200	Weak transcription	Fetal Muscle Leg	muscle
48	chr12:42785400-42836000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:42786000-42794000	Weak transcription	Fetal Stomach	stomach
50	chr12:42786000-42794200	Weak transcription	Fetal Intestine Small	intestine

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