Variant report

Variant	rs299459
Chromosome Location	chr12:29697218-29697219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10400534	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs10400541	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs10771545	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10771546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771547	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771549	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843443	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843446	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050270	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11050271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11050273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11050278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11050280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11050281	0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11050284	0.85[ASN][1000 genomes]
rs11050288	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050291	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050292	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050293	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050295	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050296	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050298	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050299	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050300	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050301	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050302	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11611194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12579805	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12581671	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12810291	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12819780	0.91[JPT][hapmap]
rs12820673	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1326758	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs1409616	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs159696	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs159701	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs159703	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs159704	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs159705	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs159707	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs159708	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs159709	0.95[JPT][hapmap]
rs159714	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs1988548	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2060569	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2113879	0.88[CEU][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2113880	0.88[CEU][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2288131	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs2288132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288133	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288230	0.84[EUR][1000 genomes]
rs2350532	0.88[CEU][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2553077	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2766605	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2766606	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs299444	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs299445	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs299455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs299456	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs299457	0.91[ASN][1000 genomes]
rs299462	1.00[CEU][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes]
rs299463	0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs299464	0.93[EUR][1000 genomes]
rs299465	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs299466	1.00[CEU][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes]
rs299472	1.00[CEU][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs299475	0.87[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs34020170	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34187264	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34555972	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35111056	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35536095	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35741143	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs375109	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3910442	0.94[MEX][hapmap]
rs4931201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931204	0.85[ASN][1000 genomes]
rs60500145	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6487837	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7294502	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7295284	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs7301491	0.88[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]
rs7306397	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7310555	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7310895	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7314549	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971202	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9300191	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9300192	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9738399	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs994172	0.81[CHB][hapmap];0.91[JPT][hapmap]

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	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
6	nsv983497	chr12:29696128-29702801	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29650400-29699000	Weak transcription	Right Ventricle	heart
2	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:29668800-29706000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:29670600-29697400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:29670600-29699000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:29673600-29708800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:29682200-29697400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:29688200-29699000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:29688200-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:29689400-29700000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:29691000-29705800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:29691200-29698800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:29691200-29709200	Weak transcription	HMEC	breast
15	chr12:29693000-29705600	Weak transcription	Hela-S3	cervix
16	chr12:29695400-29697400	Enhancers	Fetal Stomach	stomach
17	chr12:29695800-29698000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:29695800-29699000	Weak transcription	Psoas Muscle	Psoas
19	chr12:29696400-29698800	Weak transcription	Ovary	ovary
20	chr12:29696400-29706000	Weak transcription	Aorta	Aorta
21	chr12:29696600-29698000	Enhancers	NHLF	lung
22	chr12:29696600-29698800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:29696600-29699000	Weak transcription	Right Atrium	heart
24	chr12:29696600-29699000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:29696600-29699200	Weak transcription	HSMMtube	muscle
26	chr12:29696600-29700000	Weak transcription	Adipose Nuclei	Adipose
27	chr12:29696600-29705600	Weak transcription	Osteobl	bone
28	chr12:29696800-29698600	Weak transcription	NHDF-Ad	bronchial
29	chr12:29696800-29698800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:29696800-29699000	Weak transcription	HSMM	muscle
31	chr12:29696800-29699600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:29697200-29697400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:29697200-29697400	Enhancers	Left Ventricle	heart
34	chr12:29697200-29697600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:29697200-29697800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr12:29697200-29697800	Enhancers	Spleen	Spleen
37	chr12:29697200-29698000	Enhancers	H9 Cell Line	embryonic stem cell
38	chr12:29697200-29698000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr12:29697200-29698000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:29697200-29698000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:29697200-29699200	Enhancers	GM12878-XiMat	blood
42	chr12:29697200-29701400	Enhancers	Fetal Muscle Leg	muscle

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