Variant report

Variant	rs3850979
Chromosome Location	chr12:31799979-31799980
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	KAP1	chr12:31799937-31800473	HEK293	kidney:	n/a	n/a
2	MXI1	chr12:31799823-31800520	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr12:31799974-31800469	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
METTL20	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10844000	0.84[ASW][hapmap]
rs11051541	1.00[JPT][hapmap]
rs11051545	0.84[ASW][hapmap];1.00[JPT][hapmap]
rs12813042	1.00[JPT][hapmap]
rs35517071	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4272861	1.00[JPT][hapmap]
rs7134951	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7300260	0.84[ASW][hapmap]
rs7302229	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7960893	1.00[JPT][hapmap]

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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3850979	AMN1	cis	cerebellum	SCAN
rs3850979	C12orf72	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31783400-31803000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:31783400-31803000	Weak transcription	Fetal Intestine Small	intestine
3	chr12:31789600-31803000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:31789800-31801200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:31789800-31803000	Weak transcription	Adipose Nuclei	Adipose
6	chr12:31797000-31800000	Enhancers	Hela-S3	cervix
7	chr12:31797200-31800400	Enhancers	Ovary	ovary
8	chr12:31797400-31800600	Enhancers	Primary B cells from cord blood	blood
9	chr12:31797600-31803000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:31798000-31800000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:31798000-31800000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:31798200-31800000	Weak transcription	HSMMtube	muscle
13	chr12:31798200-31802200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:31798400-31800000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:31798400-31800200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:31798400-31800400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:31798400-31800600	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:31798400-31800600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:31798800-31800600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:31798800-31800600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:31798800-31803200	Weak transcription	HepG2	liver
22	chr12:31799000-31800800	Enhancers	Primary hematopoietic stem cells	blood
23	chr12:31799000-31803000	Weak transcription	Pancreas	Pancrea
24	chr12:31799200-31800000	Weak transcription	Fetal Brain Male	brain
25	chr12:31799200-31800200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:31799200-31800200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:31799200-31803400	Weak transcription	A549	lung
28	chr12:31799200-31811400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:31799400-31800400	Enhancers	Placenta	Placenta
30	chr12:31799400-31800800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:31799400-31803600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:31799600-31800200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr12:31799600-31800400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:31799600-31800600	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr12:31799600-31804400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr12:31799800-31800000	Enhancers	Fetal Kidney	kidney
37	chr12:31799800-31800400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr12:31799800-31800600	Enhancers	HMEC	breast
39	chr12:31799800-31800600	Enhancers	NHEK	skin

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