Variant report

Variant	rs2254945
Chromosome Location	chr12:29721945-29721946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10400534	1.00[CEU][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10400541	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs10492312	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771551	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771552	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10771553	0.81[JPT][hapmap]
rs10843445	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050284	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11050285	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12372765	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1326758	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs1409615	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs148898	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1529908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159687	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159690	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159694	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs159695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159696	0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs159697	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159699	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs159700	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs159702	0.89[YRI][hapmap]
rs159713	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap]
rs159716	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs177254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1863224	0.95[JPT][hapmap]
rs2081429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2113879	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[ASN][1000 genomes]
rs2113880	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[ASN][1000 genomes]
rs2162033	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2194819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2209660	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2209661	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2209662	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2225065	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2243623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288131	0.86[CEU][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2288230	0.89[ASN][1000 genomes]
rs2350532	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs2710775	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2766599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2766600	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2766602	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2766604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299444	0.95[CEU][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs299445	0.95[CEU][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs299453	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299454	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299456	0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs299457	0.88[EUR][1000 genomes]
rs299458	0.81[ASN][1000 genomes]
rs299462	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs299463	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs299464	0.89[ASN][1000 genomes]
rs299465	0.95[CHB][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs299466	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs299467	0.92[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299468	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299469	0.88[AMR][1000 genomes]
rs299470	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299471	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299472	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs299473	0.88[YRI][hapmap]
rs299475	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs299479	0.92[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299487	0.92[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs366998	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3910440	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs3910441	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4931204	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57231427	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7959535	0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs7960782	0.95[JPT][hapmap]
rs7965227	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs994171	0.87[CHB][hapmap];0.95[JPT][hapmap]

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	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
3	chr12:29709800-29756200	Weak transcription	HMEC	breast
4	chr12:29712600-29722200	Weak transcription	Colonic Mucosa	Colon
5	chr12:29712600-29734600	Weak transcription	Liver	Liver
6	chr12:29712800-29722200	Weak transcription	Brain Germinal Matrix	brain
7	chr12:29713200-29726400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:29713200-29726600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:29713200-29731200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:29715400-29722200	Weak transcription	Fetal Lung	lung
12	chr12:29715400-29731200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:29715800-29724800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:29716400-29722200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:29717400-29722200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:29717600-29725000	Weak transcription	Aorta	Aorta
18	chr12:29717600-29727400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:29717600-29727800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:29717600-29734800	Weak transcription	NHLF	lung
21	chr12:29717600-29736400	Weak transcription	Psoas Muscle	Psoas
22	chr12:29717800-29732200	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:29718200-29725400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:29718600-29727600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:29718800-29723000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:29719400-29722800	Enhancers	Fetal Kidney	kidney
27	chr12:29719400-29724000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:29719600-29722200	Weak transcription	Fetal Stomach	stomach
29	chr12:29719600-29724600	Weak transcription	Right Ventricle	heart
30	chr12:29719600-29724600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:29719800-29722200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:29719800-29724800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:29720000-29724200	Weak transcription	Left Ventricle	heart
34	chr12:29720000-29731400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:29720000-29731800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:29720200-29722600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:29720200-29724200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:29720200-29724200	Weak transcription	Spleen	Spleen
39	chr12:29720200-29724400	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:29720200-29728600	Weak transcription	Gastric	stomach
41	chr12:29720200-29735000	Weak transcription	NHDF-Ad	bronchial
42	chr12:29720200-29735800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:29720200-29743600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:29720400-29723400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:29720800-29724000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:29720800-29724000	Weak transcription	Fetal Heart	heart
47	chr12:29721000-29722000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:29721200-29722800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:29721600-29722400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr12:29721600-29722600	Enhancers	Duodenum Smooth Muscle	Duodenum

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