Variant report

Variant	rs12229802
Chromosome Location	chr12:29823887-29823888
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10128913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10743669	0.81[JPT][hapmap]
rs10771561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10771564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10771566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10771567	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10843475	0.83[CEU][hapmap]
rs11050354	0.94[YRI][hapmap]
rs12228730	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2033027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2033028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2033032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2033035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2033036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2033037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2033041	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4617668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs759888	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs759890	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs7964894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7965351	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	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
3	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
4	nsv870004	chr12:29762415-29825798	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29778400-29826000	Weak transcription	Fetal Kidney	kidney
2	chr12:29793400-29826200	Weak transcription	NHLF	lung
3	chr12:29794200-29825600	Weak transcription	Fetal Stomach	stomach
4	chr12:29794200-29825600	Weak transcription	HMEC	breast
5	chr12:29794400-29831800	Weak transcription	Ovary	ovary
6	chr12:29794800-29825600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:29794800-29829400	Weak transcription	Hela-S3	cervix
8	chr12:29803600-29824600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:29805600-29824600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:29806800-29829200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:29810200-29825400	Weak transcription	HSMMtube	muscle
12	chr12:29810400-29825200	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:29811000-29825200	Weak transcription	Fetal Heart	heart
14	chr12:29813400-29825200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:29813400-29825600	Weak transcription	HSMM	muscle
16	chr12:29813600-29825000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:29814000-29824600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:29814000-29824600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:29816200-29825200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:29816200-29825200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:29816200-29825600	Weak transcription	Left Ventricle	heart
22	chr12:29816600-29840400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:29820200-29851600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:29820400-29844200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:29821000-29827400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:29821200-29825400	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:29821200-29825600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:29821200-29829600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:29821400-29828600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:29821400-29829800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:29822200-29825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:29822400-29824800	Weak transcription	Psoas Muscle	Psoas
33	chr12:29822400-29828200	Weak transcription	Aorta	Aorta
34	chr12:29822400-29840200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:29823000-29829400	Weak transcription	Right Atrium	heart
36	chr12:29823600-29824800	Weak transcription	Spleen	Spleen
37	chr12:29823800-29825600	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links