Variant report

Variant	rs12820931
Chromosome Location	chr12:48190985-48190986
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	POLR2A	chr12:48190690-48191008	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr12:48190623-48191039	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48188175..48191554-chr12:48193435..48196727,4	K562	blood:
2	chr12:48178543..48181297-chr12:48188884..48191254,2	MCF-7	breast:
3	chr12:48185532..48188230-chr12:48190499..48192476,2	MCF-7	breast:
4	chr12:48189801..48192415-chr12:48195227..48196888,2	K562	blood:

Variant related genes	Relation type
HDAC7	TF binding region
ENSG00000061273	Chromatin interaction
ENSG00000268069	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11837686	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12814620	1.00[ASN][1000 genomes]
rs12828203	1.00[ASN][1000 genomes]
rs12828577	1.00[ASN][1000 genomes]
rs17122326	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs34248545	1.00[ASN][1000 genomes]
rs34379708	1.00[ASN][1000 genomes]
rs34785684	1.00[ASN][1000 genomes]
rs35392237	1.00[ASN][1000 genomes]
rs6580638	1.00[ASN][1000 genomes]
rs71462981	1.00[ASN][1000 genomes]
rs7299689	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7303453	1.00[ASN][1000 genomes]
rs7971594	1.00[ASN][1000 genomes]
rs7980930	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	esv3693398	chr12:48186738-48215749	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12820931	RAPGEF3	cis	parietal	SCAN
rs12820931	RAPGEF3	cis	cerebellum	SCAN
rs12820931	MLL2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48168200-48195200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:48173000-48192400	Weak transcription	Right Atrium	heart
3	chr12:48173200-48191200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:48173800-48193800	Strong transcription	Gastric	stomach
5	chr12:48173800-48195400	Strong transcription	Fetal Stomach	stomach
6	chr12:48174000-48193000	Strong transcription	Placenta	Placenta
7	chr12:48174600-48191600	Strong transcription	Thymus	Thymus
8	chr12:48174600-48192200	Strong transcription	Lung	lung
9	chr12:48174600-48192600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:48174600-48193200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:48174600-48193400	Strong transcription	Brain Germinal Matrix	brain
12	chr12:48174600-48195600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48174800-48191400	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:48174800-48192000	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:48174800-48192000	Strong transcription	Ovary	ovary
16	chr12:48174800-48192400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:48174800-48192800	Strong transcription	Primary T cells from cord blood	blood
18	chr12:48174800-48194600	Strong transcription	Fetal Intestine Large	intestine
19	chr12:48175000-48191800	Strong transcription	Colonic Mucosa	Colon
20	chr12:48175000-48193000	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr12:48175000-48193000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:48175000-48193200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:48175000-48193200	Strong transcription	NHLF	lung
24	chr12:48175000-48193200	Strong transcription	Osteobl	bone
25	chr12:48175000-48193400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:48175200-48191400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:48175200-48193600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:48175400-48191000	Strong transcription	Primary hematopoietic stem cells	blood
29	chr12:48175400-48191400	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr12:48175400-48191400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr12:48175400-48192800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:48175600-48191000	Strong transcription	Hela-S3	cervix
33	chr12:48175600-48191400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:48175600-48191400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr12:48175600-48192400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:48175600-48192800	Strong transcription	Aorta	Aorta
37	chr12:48175600-48195000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:48175600-48195800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:48175800-48191000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:48175800-48191000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:48175800-48191200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:48175800-48191400	Strong transcription	Rectal Smooth Muscle	rectum
43	chr12:48175800-48193000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr12:48176000-48192400	Strong transcription	Left Ventricle	heart
45	chr12:48176000-48192600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:48176200-48191200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:48176400-48193400	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr12:48176600-48191600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:48176800-48191800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr12:48176800-48192000	Strong transcription	A549	lung

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