Variant report

Variant	rs12262878
Chromosome Location	chr10:96971504-96971505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 169 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:164)

rs_ID	r²[population]
rs10128123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10218877	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10509682	0.93[ASN][1000 genomes]
rs10509683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786186	0.93[ASN][1000 genomes]
rs10786187	0.86[ASN][1000 genomes]
rs10786188	0.93[ASN][1000 genomes]
rs10786189	0.86[ASN][1000 genomes]
rs10786190	0.86[ASN][1000 genomes]
rs10882542	0.93[ASN][1000 genomes]
rs10882543	0.86[ASN][1000 genomes]
rs10882546	0.86[ASN][1000 genomes]
rs10882551	0.93[ASN][1000 genomes]
rs10882562	0.93[ASN][1000 genomes]
rs10882564	0.93[ASN][1000 genomes]
rs10882565	0.93[ASN][1000 genomes]
rs10882566	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10882568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882569	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188189	0.86[ASN][1000 genomes]
rs11188190	0.86[ASN][1000 genomes]
rs11188192	0.86[ASN][1000 genomes]
rs11188196	0.86[ASN][1000 genomes]
rs11188197	0.86[ASN][1000 genomes]
rs11188200	0.86[ASN][1000 genomes]
rs11188214	0.93[ASN][1000 genomes]
rs11188219	0.93[ASN][1000 genomes]
rs11188223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11188225	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11188227	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188238	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11572093	0.82[CHB][hapmap]
rs11596737	0.81[CEU][hapmap]
rs11596853	0.81[CEU][hapmap]
rs11598953	1.00[JPT][hapmap]
rs11599884	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11872	1.00[JPT][hapmap]
rs12245722	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261370	0.86[ASN][1000 genomes]
rs12266386	0.82[ASN][1000 genomes]
rs12354433	0.93[ASN][1000 genomes]
rs12413028	0.92[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs12415795	0.92[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs12764831	1.00[JPT][hapmap]
rs12769820	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12782731	0.86[ASN][1000 genomes]
rs12783947	0.96[EUR][1000 genomes]
rs1341164	0.82[CHB][hapmap]
rs1575930	0.86[ASN][1000 genomes]
rs16872	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17451604	0.93[ASN][1000 genomes]
rs17524438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934955	0.82[CHB][hapmap]
rs1934957	0.82[CHB][hapmap]
rs1934982	0.82[CHB][hapmap]
rs1934983	0.82[CHB][hapmap]
rs2071426	0.85[CHB][hapmap]
rs2185571	0.82[CHB][hapmap]
rs2449809	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2449810	0.86[ASN][1000 genomes]
rs2478477	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2478478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2478479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2478480	0.93[ASN][1000 genomes]
rs2901829	0.86[ASN][1000 genomes]
rs34999658	0.93[ASN][1000 genomes]
rs35306243	0.93[ASN][1000 genomes]
rs35999600	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532969	0.86[ASN][1000 genomes]
rs489807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs509736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs513661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs519833	0.93[ASN][1000 genomes]
rs585381	0.86[ASN][1000 genomes]
rs589801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs591157	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs591171	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs592055	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs594402	0.86[ASN][1000 genomes]
rs594448	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs595420	0.93[ASN][1000 genomes]
rs595478	0.93[ASN][1000 genomes]
rs600929	0.93[ASN][1000 genomes]
rs602941	0.93[ASN][1000 genomes]
rs604022	0.86[ASN][1000 genomes]
rs604373	0.86[ASN][1000 genomes]
rs610046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs610579	0.82[ASN][1000 genomes]
rs610837	0.93[ASN][1000 genomes]
rs611343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs611371	0.93[ASN][1000 genomes]
rs611416	0.86[ASN][1000 genomes]
rs612490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs613340	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs614682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs61871367	0.89[EUR][1000 genomes]
rs620196	0.86[ASN][1000 genomes]
rs621299	0.93[ASN][1000 genomes]
rs626415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs627173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs627719	0.93[ASN][1000 genomes]
rs628102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs631107	0.87[ASN][1000 genomes]
rs632113	0.86[ASN][1000 genomes]
rs632361	0.93[ASN][1000 genomes]
rs632979	0.89[ASN][1000 genomes]
rs633345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs634269	0.86[ASN][1000 genomes]
rs637465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs637724	0.86[ASN][1000 genomes]
rs637939	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs638895	0.86[ASN][1000 genomes]
rs641198	0.86[ASN][1000 genomes]
rs644437	0.86[ASN][1000 genomes]
rs646845	0.86[ASN][1000 genomes]
rs648638	0.86[ASN][1000 genomes]
rs648695	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs649770	0.90[ASN][1000 genomes]
rs6583967	0.82[CHB][hapmap]
rs6583980	0.86[ASN][1000 genomes]
rs659949	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs660026	0.93[ASN][1000 genomes]
rs663473	0.86[ASN][1000 genomes]
rs664093	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs666679	0.86[ASN][1000 genomes]
rs666786	0.86[ASN][1000 genomes]
rs667499	0.89[ASN][1000 genomes]
rs669360	0.93[ASN][1000 genomes]
rs672428	0.86[ASN][1000 genomes]
rs672860	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs675332	0.86[ASN][1000 genomes]
rs678165	0.86[ASN][1000 genomes]
rs679025	0.86[ASN][1000 genomes]
rs680918	0.86[ASN][1000 genomes]
rs682477	0.86[ASN][1000 genomes]
rs685607	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs688706	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs689207	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs695217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs701886	0.93[ASN][1000 genomes]
rs7079861	0.86[ASN][1000 genomes]
rs7082502	0.86[ASN][1000 genomes]
rs7087492	0.86[ASN][1000 genomes]
rs7087618	0.86[ASN][1000 genomes]
rs7089303	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7094658	0.86[ASN][1000 genomes]
rs752415	0.86[ASN][1000 genomes]
rs752416	0.86[ASN][1000 genomes]
rs752417	0.93[ASN][1000 genomes]
rs7907627	0.86[ASN][1000 genomes]
rs7907827	0.86[ASN][1000 genomes]
rs7909072	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7921561	0.86[ASN][1000 genomes]
rs815250	0.93[ASN][1000 genomes]
rs815265	0.86[ASN][1000 genomes]
rs815266	0.86[ASN][1000 genomes]
rs815268	0.86[ASN][1000 genomes]
rs815269	0.86[ASN][1000 genomes]
rs815270	0.86[ASN][1000 genomes]
rs943313	0.86[ASN][1000 genomes]
rs943315	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv21432	chr10:96856006-96996043	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1834151	chr10:96925446-96992955	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12262878	PDLIM1	cis	cerebellum	SCAN
rs12262878	PIPSL	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96944200-96990400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr10:96949800-96980600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr10:96952800-96974600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:96956000-96973200	Weak transcription	Fetal Stomach	stomach
5	chr10:96956200-96979000	Weak transcription	Pancreas	Pancrea
6	chr10:96956200-96990400	Weak transcription	Aorta	Aorta
7	chr10:96960200-96988800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:96961200-96974600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:96961800-96975200	Weak transcription	Primary B cells from cord blood	blood
10	chr10:96961800-96989400	Weak transcription	Primary T cells from cord blood	blood
11	chr10:96962000-96990000	Weak transcription	Fetal Intestine Small	intestine
12	chr10:96964000-96972400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr10:96965000-96988000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr10:96965400-96983000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:96965400-96989400	Weak transcription	Fetal Intestine Large	intestine
16	chr10:96969200-96979400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr10:96969200-96979600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr10:96969200-96990200	Weak transcription	Left Ventricle	heart
19	chr10:96969400-96974800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr10:96969400-96977400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr10:96969400-96980200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr10:96969400-96980200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr10:96969400-96980400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr10:96969400-96981600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr10:96969400-96984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:96969400-96990400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr10:96970000-96972800	Weak transcription	Stomach Mucosa	stomach
28	chr10:96970200-96992400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr10:96970400-96972600	Strong transcription	Fetal Thymus	thymus
30	chr10:96970800-96972400	Enhancers	NHDF-Ad	bronchial
31	chr10:96970800-96972600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr10:96970800-96974200	Weak transcription	NH-A	brain
33	chr10:96971000-96972000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr10:96971000-96972400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr10:96971000-96972400	Enhancers	HSMMtube	muscle
36	chr10:96971200-96972200	Enhancers	HMEC	breast
37	chr10:96971400-96971600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr10:96971400-96971600	Enhancers	A549	lung
39	chr10:96971400-96972000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr10:96971400-96972000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr10:96971400-96972000	Enhancers	NHEK	skin
42	chr10:96971400-96972000	Enhancers	NHLF	lung
43	chr10:96971400-96972200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:96971400-96972200	Enhancers	Adipose Nuclei	Adipose
45	chr10:96971400-96972400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr10:96971400-96972400	Enhancers	HSMM	muscle
47	chr10:96971400-96972400	Enhancers	Osteobl	bone

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