Variant report

Variant	rs299444
Chromosome Location	chr12:29682475-29682476
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10400534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10400541	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10492312	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10771545	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs10771546	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs10771547	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs10771549	0.87[ASN][1000 genomes]
rs10771550	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10771551	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10771552	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10843443	0.88[ASN][1000 genomes]
rs10843445	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11050270	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs11050271	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs11050273	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs11050278	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs11050280	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs11050281	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs11050284	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050285	0.95[CEU][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11050292	0.90[CHB][hapmap]
rs11050293	0.90[CHB][hapmap]
rs11050297	0.94[CHB][hapmap]
rs11050298	0.83[ASN][1000 genomes]
rs11050299	0.90[CHB][hapmap]
rs11050300	0.90[CHB][hapmap]
rs11050301	0.90[CHB][hapmap]
rs11050302	0.90[CHB][hapmap]
rs11050308	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11611194	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs12371221	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs12581671	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12820673	0.86[ASN][1000 genomes]
rs1326758	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs148898	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1529908	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs159685	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs159687	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs159689	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs159690	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs159694	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs159695	0.95[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs159696	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs159697	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs159698	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs159701	0.85[CHB][hapmap]
rs159703	0.90[CHB][hapmap]
rs159704	0.85[CHB][hapmap]
rs159705	0.85[CHB][hapmap]
rs159707	0.81[CHB][hapmap]
rs159708	0.81[CHB][hapmap]
rs159709	0.82[CHB][hapmap]
rs159713	0.82[YRI][hapmap]
rs177254	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1988548	0.90[CHB][hapmap]
rs2060569	0.87[ASN][1000 genomes]
rs2081429	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2162033	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2194819	0.95[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2243623	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2254945	0.95[CEU][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2288131	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288132	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs2288133	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs2710775	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2766599	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2766600	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2766601	0.95[CEU][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2766602	0.95[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2766604	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs299445	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]
rs299453	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs299454	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs299455	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs299456	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299457	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299459	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs299467	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs299468	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs299469	0.89[AMR][1000 genomes]
rs299470	1.00[CEU][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs299471	0.91[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs299479	1.00[CEU][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs299487	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34555972	0.82[ASN][1000 genomes]
rs35111056	0.88[ASN][1000 genomes]
rs35741143	0.87[ASN][1000 genomes]
rs366998	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs375109	0.87[ASN][1000 genomes]
rs3910440	0.87[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs3910441	0.86[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs4931201	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs4931204	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57231427	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6487837	0.91[ASN][1000 genomes]
rs7294502	0.90[CHB][hapmap]
rs7301491	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs7306397	0.87[ASN][1000 genomes]
rs7310555	0.90[CHB][hapmap]
rs7310895	0.90[CHB][hapmap]
rs7311193	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7314549	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs7971202	0.87[ASN][1000 genomes]
rs9300191	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs9300192	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29650400-29699000	Weak transcription	Right Ventricle	heart
2	chr12:29658400-29690200	Weak transcription	HMEC	breast
3	chr12:29660800-29690000	Weak transcription	NHDF-Ad	bronchial
4	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:29667200-29695600	Weak transcription	Ovary	ovary
6	chr12:29668600-29690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:29668600-29695800	Weak transcription	Aorta	Aorta
8	chr12:29668800-29706000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:29670600-29687000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:29670600-29687800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:29670600-29697400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:29670600-29699000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:29671000-29688000	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:29671000-29697200	Weak transcription	Spleen	Spleen
16	chr12:29671600-29695400	Weak transcription	Fetal Stomach	stomach
17	chr12:29671600-29697200	Weak transcription	Left Ventricle	heart
18	chr12:29672600-29686000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:29673600-29708800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:29673800-29687600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:29675400-29686400	Weak transcription	HSMM	muscle
22	chr12:29675800-29689400	Weak transcription	Hela-S3	cervix
23	chr12:29676400-29683200	Weak transcription	Psoas Muscle	Psoas
24	chr12:29678000-29686600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:29678000-29690000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:29678400-29695000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:29680600-29690400	Weak transcription	Fetal Kidney	kidney
28	chr12:29680800-29682800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:29681600-29686400	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:29681600-29686800	Weak transcription	HSMMtube	muscle
31	chr12:29681600-29690400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:29681600-29695600	Weak transcription	Adipose Nuclei	Adipose
33	chr12:29681600-29695800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:29682200-29683200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:29682200-29697400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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