Variant report

Variant	rs12824420
Chromosome Location	chr12:29715926-29715927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29713988..29716071-chr12:29717724..29720269,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11837554	1.00[CHB][hapmap]
rs12312423	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422557	1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423770	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423941	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424239	1.00[CHB][hapmap]
rs12424383	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424502	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425004	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810686	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811228	1.00[CHB][hapmap]
rs12813081	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816393	1.00[CHB][hapmap]
rs12817852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820766	1.00[EUR][1000 genomes]
rs12820809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822845	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12824107	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826187	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826210	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826354	1.00[EUR][1000 genomes]
rs12826633	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826911	1.00[AMR][1000 genomes]
rs12828726	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831066	1.00[EUR][1000 genomes]
rs159684	1.00[CHB][hapmap]
rs28862044	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299450	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs299484	1.00[CHB][hapmap]
rs34051575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34211411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34265395	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34310782	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34377769	1.00[EUR][1000 genomes]
rs34384320	1.00[AMR][1000 genomes]
rs34401020	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34564434	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34598140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34689118	1.00[EUR][1000 genomes]
rs34769239	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34769930	1.00[EUR][1000 genomes]
rs34818263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34867963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906400	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35047658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35205102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35343129	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35372963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35425592	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35439792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35477340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35666547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35725284	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35856698	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35957198	1.00[EUR][1000 genomes]
rs36043605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36070392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36093094	1.00[EUR][1000 genomes]
rs3825242	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134105	1.00[EUR][1000 genomes]
rs71453743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71453744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71453746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71453747	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71453748	1.00[EUR][1000 genomes]
rs71453749	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7316470	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:29700400-29719000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
5	chr12:29705000-29716000	Weak transcription	Spleen	Spleen
6	chr12:29706600-29716200	Weak transcription	Aorta	Aorta
7	chr12:29709800-29756200	Weak transcription	HMEC	breast
8	chr12:29710200-29717800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:29711400-29716600	Enhancers	Stomach Mucosa	stomach
10	chr12:29711400-29718200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr12:29711800-29716600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:29711800-29720800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:29712600-29722200	Weak transcription	Colonic Mucosa	Colon
14	chr12:29712600-29734600	Weak transcription	Liver	Liver
15	chr12:29712800-29722200	Weak transcription	Brain Germinal Matrix	brain
16	chr12:29713200-29719800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:29713200-29719800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:29713200-29726400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:29713200-29726600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:29713200-29731200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:29714200-29716200	Enhancers	HSMM	muscle
23	chr12:29714200-29716600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:29714200-29717400	Enhancers	Fetal Kidney	kidney
25	chr12:29714200-29717800	Enhancers	HSMMtube	muscle
26	chr12:29714400-29716600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:29714400-29716600	Enhancers	NHDF-Ad	bronchial
28	chr12:29714400-29717400	Enhancers	Adipose Nuclei	Adipose
29	chr12:29714400-29717400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr12:29714400-29717600	Enhancers	NHLF	lung
31	chr12:29714400-29717800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:29714600-29717400	Enhancers	Fetal Heart	heart
33	chr12:29715000-29716000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:29715000-29716200	Enhancers	Osteobl	bone
35	chr12:29715000-29716400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:29715000-29716800	Enhancers	Ovary	ovary
37	chr12:29715000-29717200	Enhancers	Fetal Stomach	stomach
38	chr12:29715200-29716000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:29715200-29716400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:29715200-29717000	Enhancers	HUVEC	blood vessel
41	chr12:29715200-29717400	Enhancers	Fetal Muscle Leg	muscle
42	chr12:29715200-29717600	Enhancers	Left Ventricle	heart
43	chr12:29715200-29717600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr12:29715200-29717800	Enhancers	Colon Smooth Muscle	Colon
45	chr12:29715400-29716400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:29715400-29716600	Enhancers	Hela-S3	cervix
47	chr12:29715400-29718000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:29715400-29721400	Weak transcription	Esophagus	oesophagus
49	chr12:29715400-29722200	Weak transcription	Fetal Lung	lung
50	chr12:29715400-29731200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links