Variant report

Variant	rs16934564
Chromosome Location	chr12:29745439-29745440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11050323	0.88[CHB][hapmap]
rs11829731	1.00[CHB][hapmap]
rs11834291	1.00[CHB][hapmap]
rs12822100	0.89[CHB][hapmap]
rs12826893	0.89[CHB][hapmap]
rs12826911	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12828728	0.89[CHB][hapmap]
rs142565	0.89[CHB][hapmap]
rs148897	1.00[CHB][hapmap]
rs159688	0.89[CHB][hapmap]
rs159691	0.89[CHB][hapmap]
rs159692	0.89[CHB][hapmap]
rs16934418	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16934523	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16934537	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16934569	1.00[CHB][hapmap]
rs16934597	1.00[CHB][hapmap]
rs16934635	0.89[CHB][hapmap]
rs299477	0.89[CHB][hapmap]
rs299478	0.89[CHB][hapmap]
rs299482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs299483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs299485	0.89[CHB][hapmap]
rs7301943	1.00[CHB][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	nsv1051913	chr12:29741676-29770807	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29709800-29756200	Weak transcription	HMEC	breast
2	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:29726000-29751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:29731800-29769600	Weak transcription	Hela-S3	cervix
5	chr12:29735400-29745800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:29736000-29752200	Weak transcription	HSMM	muscle
7	chr12:29736800-29762800	Weak transcription	Fetal Stomach	stomach
8	chr12:29737000-29748400	Weak transcription	Spleen	Spleen
9	chr12:29737200-29746800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:29737200-29748400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:29737200-29761800	Weak transcription	Right Ventricle	heart
12	chr12:29737200-29762400	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:29737200-29762800	Weak transcription	Psoas Muscle	Psoas
14	chr12:29741000-29748200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:29742200-29746000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:29742600-29746200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:29742800-29750200	Weak transcription	Aorta	Aorta
18	chr12:29742800-29752200	Weak transcription	HSMMtube	muscle
19	chr12:29743200-29751800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:29743200-29769800	Weak transcription	NHLF	lung
21	chr12:29743600-29746200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr12:29744000-29746200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr12:29744200-29745600	Enhancers	Fetal Lung	lung
24	chr12:29744400-29747600	Weak transcription	Lung	lung
25	chr12:29744400-29790800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:29744600-29747800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:29744600-29749600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:29744600-29752600	Weak transcription	Left Ventricle	heart
29	chr12:29744600-29754200	Weak transcription	Brain Anterior Caudate	brain
30	chr12:29744600-29765400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:29744600-29791000	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:29744800-29745600	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr12:29744800-29745600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:29744800-29747600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:29744800-29749000	Enhancers	Liver	Liver
36	chr12:29744800-29764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:29744800-29778200	Weak transcription	Ovary	ovary
38	chr12:29745000-29745800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr12:29745000-29746000	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr12:29745000-29746200	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:29745000-29746400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr12:29745000-29746400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr12:29745000-29749200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:29745200-29747600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr12:29745200-29748200	Weak transcription	Adipose Nuclei	Adipose
46	chr12:29745200-29751000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:29745200-29751600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:29745200-29755000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:29745200-29762000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:29745400-29750000	Weak transcription	Fetal Heart	heart

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