Variant report

Variant	rs16934577
Chromosome Location	chr12:29749303-29749304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11050309	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11050313	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11050314	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11835297	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11837770	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11837812	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300479	1.00[AMR][1000 genomes]
rs12303679	1.00[AMR][1000 genomes]
rs12314431	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314860	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12317132	0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16934608	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16934622	0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59063950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7134105	1.00[AMR][1000 genomes]
rs7134157	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7315908	1.00[AMR][1000 genomes]
rs73268031	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73281235	1.00[AMR][1000 genomes]
rs7973359	0.80[AFR][1000 genomes];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	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:45 , 50 per page) page: 1

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	chr12:29736000-29752200	Weak transcription	HSMM	muscle
6	chr12:29736800-29762800	Weak transcription	Fetal Stomach	stomach
7	chr12:29737200-29761800	Weak transcription	Right Ventricle	heart
8	chr12:29737200-29762400	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:29737200-29762800	Weak transcription	Psoas Muscle	Psoas
10	chr12:29742800-29750200	Weak transcription	Aorta	Aorta
11	chr12:29742800-29752200	Weak transcription	HSMMtube	muscle
12	chr12:29743200-29751800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:29743200-29769800	Weak transcription	NHLF	lung
14	chr12:29744400-29790800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr12:29744600-29749600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:29744600-29752600	Weak transcription	Left Ventricle	heart
17	chr12:29744600-29754200	Weak transcription	Brain Anterior Caudate	brain
18	chr12:29744600-29765400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:29744600-29791000	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:29744800-29764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:29744800-29778200	Weak transcription	Ovary	ovary
22	chr12:29745200-29751000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:29745200-29751600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:29745200-29755000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:29745200-29762000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:29745400-29750000	Weak transcription	Fetal Heart	heart
27	chr12:29745400-29752000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:29746000-29751000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:29746200-29752200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:29746200-29757200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:29746200-29762200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:29746400-29750800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:29746400-29751000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:29747000-29757800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:29747200-29749400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:29747200-29749400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:29747400-29756400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:29747600-29750200	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr12:29748400-29750400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr12:29748600-29751800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:29748600-29751800	Weak transcription	Adipose Nuclei	Adipose
42	chr12:29748600-29762600	Weak transcription	Spleen	Spleen
43	chr12:29749000-29751800	Weak transcription	Liver	Liver
44	chr12:29749200-29749800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:29749200-29753600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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