Variant report

Variant	rs299460
Chromosome Location	chr12:29697569-29697570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10771548	1.00[EUR][1000 genomes]
rs159682	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs159686	0.89[AFR][1000 genomes]
rs299446	1.00[EUR][1000 genomes]
rs299448	1.00[EUR][1000 genomes]
rs299449	1.00[EUR][1000 genomes]
rs299451	1.00[EUR][1000 genomes]
rs299452	1.00[EUR][1000 genomes]
rs299481	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs299486	1.00[YRI][hapmap]
rs41322250	1.00[YRI][hapmap]
rs58290969	1.00[AMR][1000 genomes]
rs7134177	0.89[AFR][1000 genomes]
rs73263805	1.00[AMR][1000 genomes]
rs73263811	1.00[AMR][1000 genomes]
rs73263816	1.00[AMR][1000 genomes]
rs73263829	1.00[AMR][1000 genomes]
rs73263831	1.00[AMR][1000 genomes]
rs73263838	1.00[AMR][1000 genomes]
rs73263901	1.00[AMR][1000 genomes]
rs73266083	1.00[AMR][1000 genomes]
rs73266085	1.00[AMR][1000 genomes]
rs73266100	1.00[AMR][1000 genomes]
rs73266101	1.00[AMR][1000 genomes]
rs73268003	1.00[AMR][1000 genomes]

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:49 , 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	chr12:29670600-29699000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:29673600-29708800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:29688200-29699000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:29688200-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:29689400-29700000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:29691000-29705800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:29691200-29698800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:29691200-29709200	Weak transcription	HMEC	breast
13	chr12:29693000-29705600	Weak transcription	Hela-S3	cervix
14	chr12:29695800-29698000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:29695800-29699000	Weak transcription	Psoas Muscle	Psoas
16	chr12:29696400-29698800	Weak transcription	Ovary	ovary
17	chr12:29696400-29706000	Weak transcription	Aorta	Aorta
18	chr12:29696600-29698000	Enhancers	NHLF	lung
19	chr12:29696600-29698800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:29696600-29699000	Weak transcription	Right Atrium	heart
21	chr12:29696600-29699000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:29696600-29699200	Weak transcription	HSMMtube	muscle
23	chr12:29696600-29700000	Weak transcription	Adipose Nuclei	Adipose
24	chr12:29696600-29705600	Weak transcription	Osteobl	bone
25	chr12:29696800-29698600	Weak transcription	NHDF-Ad	bronchial
26	chr12:29696800-29698800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:29696800-29699000	Weak transcription	HSMM	muscle
28	chr12:29696800-29699600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:29697200-29697600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:29697200-29697800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr12:29697200-29697800	Enhancers	Spleen	Spleen
32	chr12:29697200-29698000	Enhancers	H9 Cell Line	embryonic stem cell
33	chr12:29697200-29698000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr12:29697200-29698000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:29697200-29698000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:29697200-29699200	Enhancers	GM12878-XiMat	blood
37	chr12:29697200-29701400	Enhancers	Fetal Muscle Leg	muscle
38	chr12:29697400-29697600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:29697400-29697600	Enhancers	Duodenum Mucosa	Duodenum
40	chr12:29697400-29697600	Enhancers	Fetal Muscle Trunk	muscle
41	chr12:29697400-29697600	Genic enhancers	Left Ventricle	heart
42	chr12:29697400-29697600	Enhancers	Lung	lung
43	chr12:29697400-29698000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr12:29697400-29698200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr12:29697400-29698800	Weak transcription	Fetal Stomach	stomach
46	chr12:29697400-29699000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:29697400-29700000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr12:29697400-29700600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:29697400-29701400	Enhancers	Skeletal Muscle Male	skeletal muscle

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