Variant report

Variant	rs12815479
Chromosome Location	chr12:123430082-123430083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr12:123429616-123430093	HEK293-T-REx	kidney:	n/a	chr12:123429814-123429823 chr12:123429822-123429843

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123428831..123432471-chr12:123448558..123452277,3	K562	blood:
2	chr12:123428831..123431560-chr12:123448558..123451555,2	K562	blood:

Variant related genes	Relation type
ABCB9	TF binding region
ENSG00000150967	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1260121	1.00[CHD][hapmap]
rs1671687	1.00[CHD][hapmap]
rs1798563	1.00[CHD][hapmap]
rs1975761	1.00[CHD][hapmap]
rs2649895	1.00[CHD][hapmap]
rs2656812	1.00[CHD][hapmap]
rs7958155	1.00[CHD][hapmap]
rs7964876	0.82[AMR][1000 genomes]
rs839354	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv560491	chr12:123425575-123444422	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	esv3404104	chr12:123428049-123430847	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12815479	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs12815479	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123402800-123430800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:123403000-123444200	Weak transcription	Aorta	Aorta
3	chr12:123412800-123431800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:123412800-123449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:123413400-123449600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr12:123413600-123431400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:123413600-123450000	Weak transcription	Primary T cells from cord blood	blood
8	chr12:123414000-123432400	Weak transcription	Fetal Kidney	kidney
9	chr12:123415800-123431600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:123417400-123441800	Weak transcription	Ovary	ovary
11	chr12:123417600-123446200	Weak transcription	Fetal Lung	lung
12	chr12:123424200-123431000	Weak transcription	Fetal Intestine Large	intestine
13	chr12:123425600-123432400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr12:123425600-123432600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:123425800-123431200	Enhancers	Hela-S3	cervix
16	chr12:123426600-123432200	Enhancers	Right Atrium	heart
17	chr12:123427200-123432400	Enhancers	Fetal Muscle Leg	muscle
18	chr12:123427200-123432600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:123427200-123432600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:123427200-123432600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:123427200-123433200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:123427200-123433200	Enhancers	Stomach Mucosa	stomach
23	chr12:123427400-123432600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:123427600-123431200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:123427800-123430200	Enhancers	Right Ventricle	heart
26	chr12:123427800-123431000	Weak transcription	Small Intestine	intestine
27	chr12:123427800-123431400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:123427800-123431400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr12:123427800-123432600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:123428000-123430600	Weak transcription	Fetal Intestine Small	intestine
31	chr12:123428000-123430600	Weak transcription	GM12878-XiMat	blood
32	chr12:123428000-123430800	Weak transcription	Fetal Thymus	thymus
33	chr12:123428000-123431200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:123428000-123431200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr12:123428000-123431200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:123428200-123430200	Enhancers	HUVEC	blood vessel
37	chr12:123428200-123430600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:123428200-123430600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr12:123428400-123430600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr12:123428400-123431400	Enhancers	Adipose Nuclei	Adipose
41	chr12:123428600-123430200	Enhancers	NH-A	brain
42	chr12:123428600-123430600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:123428600-123430800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:123428600-123431200	Enhancers	NHEK	skin
45	chr12:123428600-123432600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr12:123428800-123431800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr12:123428800-123432400	Enhancers	A549	lung
48	chr12:123428800-123432400	Enhancers	HSMM	muscle
49	chr12:123428800-123432400	Enhancers	NHDF-Ad	bronchial
50	chr12:123428800-123432600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links