Variant report

Variant	rs1796398
Chromosome Location	chr12:42828323-42828324
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1043652	0.96[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1043656	0.96[CEU][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10880275	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs10880279	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs10880282	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181421	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181427	0.96[EUR][1000 genomes]
rs11181453	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181461	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[ASN][1000 genomes]
rs11181484	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12229224	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12229266	0.96[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12230583	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12231335	0.91[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12422938	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12423383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12425945	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs12578312	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1376931	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1629725	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669884	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1669888	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669890	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669891	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669894	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669895	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669897	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669898	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669899	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1669900	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669901	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669905	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669911	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669912	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669913	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669914	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1669935	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669937	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17091052	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1796354	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796355	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1796356	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1796357	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1796359	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1796360	0.97[EUR][1000 genomes]
rs1796365	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1796373	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1796374	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1796377	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1796379	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796385	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1796387	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1796395	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796396	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796397	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1961953	0.81[EUR][1000 genomes]
rs2053946	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2243465	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2406872	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2406969	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2600911	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2600912	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2600916	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2600917	0.88[EUR][1000 genomes]
rs2600918	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2708063	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2708069	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708075	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708077	0.90[EUR][1000 genomes]
rs2708506	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952653	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3213989	0.96[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3747562	0.81[CEU][hapmap]
rs3747563	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3761677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3827524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4603368	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768397	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4768398	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4768401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768412	0.92[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6582392	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7134895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs721447	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122408	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73122414	0.97[EUR][1000 genomes]
rs73122418	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7486516	0.81[EUR][1000 genomes]
rs752767	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7960176	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs896555	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs896556	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1796398	PPHLN1	cis	multi-tissue	Pritchard
rs1796398	CPNE8	cis	parietal	SCAN
rs1796398	KIF21A	cis	parietal	SCAN
rs1796398	MADP-1	cis	multi-tissue	Pritchard
rs1796398	PPHLN1	cis	Artery Tibial	GTEx
rs1796398	NELL2	cis	parietal	SCAN

Chromatin state (count:113 , 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	chr12:42767200-42836200	Weak transcription	Esophagus	oesophagus
3	chr12:42780200-42836000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:42783000-42836000	Weak transcription	Lung	lung
5	chr12:42785400-42836000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:42789600-42836200	Weak transcription	Pancreas	Pancrea
7	chr12:42793800-42840400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:42795400-42834600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr12:42795600-42834400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:42795800-42836000	Weak transcription	Thymus	Thymus
11	chr12:42796000-42833200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:42796000-42834400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:42796000-42835000	Weak transcription	HepG2	liver
14	chr12:42796000-42835800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:42796000-42836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:42796000-42836200	Weak transcription	Fetal Stomach	stomach
17	chr12:42796000-42836400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:42796000-42838000	Weak transcription	HSMMtube	muscle
19	chr12:42812200-42835000	Weak transcription	Liver	Liver
20	chr12:42813600-42834600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:42814200-42835400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:42814200-42835600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr12:42814400-42835600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:42815400-42836000	Weak transcription	Ovary	ovary
25	chr12:42816000-42834800	Weak transcription	Brain Angular Gyrus	brain
26	chr12:42816200-42858200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:42816400-42834200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:42816400-42835400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:42816400-42836000	Weak transcription	NHLF	lung
30	chr12:42816800-42835800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:42816800-42840400	Weak transcription	Fetal Kidney	kidney
32	chr12:42816800-42862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:42817000-42836600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:42817000-42840000	Weak transcription	NHDF-Ad	bronchial
35	chr12:42818000-42834800	Weak transcription	Fetal Intestine Small	intestine
36	chr12:42818000-42835600	Weak transcription	Placenta	Placenta
37	chr12:42818000-42836200	Weak transcription	Right Ventricle	heart
38	chr12:42818600-42833000	Weak transcription	Dnd41	blood
39	chr12:42818600-42835800	Weak transcription	Fetal Lung	lung
40	chr12:42818600-42836200	Weak transcription	Aorta	Aorta
41	chr12:42819800-42836200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr12:42820000-42858200	Weak transcription	Gastric	stomach
43	chr12:42820200-42853000	Weak transcription	Fetal Heart	heart
44	chr12:42820800-42836000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:42821000-42834200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:42821000-42834800	Weak transcription	GM12878-XiMat	blood
47	chr12:42821000-42834800	Weak transcription	NHEK	skin
48	chr12:42821000-42835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:42821000-42835000	Weak transcription	HMEC	breast
50	chr12:42821000-42835000	Weak transcription	Osteobl	bone

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