Variant report

Variant	rs1920412
Chromosome Location	chr12:104448618-104448619
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	TAF1	chr12:104448492-104448699	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr12:104448591-104449010	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUND	chr12:104448543-104448939	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr12:104448593-104449020	H1-hESC	embryonic stem cell:	n/a	n/a
5	BHLHE40	chr12:104448315-104448637	K562	blood:	n/a	chr12:104448457-104448470 chr12:104448458-104448467 chr12:104448459-104448468 chr12:104448459-104448468

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104448374..104451258-chr12:104456861..104459762,4	K562	blood:

Variant related genes	Relation type
GLT8D2	TF binding region
ENSG00000111727	Chromatin interaction
ENSG00000120820	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11111878	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1564892	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs17035146	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1843371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1920410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920411	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2220210	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423256	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104444000-104449000	Weak transcription	Pancreas	Pancrea
2	chr12:104444200-104449400	Weak transcription	Liver	Liver
3	chr12:104444400-104449200	Weak transcription	Fetal Heart	heart
4	chr12:104444400-104457400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:104444600-104448800	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:104444600-104449000	Weak transcription	Ovary	ovary
7	chr12:104444600-104449200	Weak transcription	NHLF	lung
8	chr12:104444600-104449400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:104444600-104449600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:104444600-104449600	Weak transcription	Fetal Lung	lung
11	chr12:104444600-104449600	Weak transcription	HSMM	muscle
12	chr12:104444600-104449600	Weak transcription	HSMMtube	muscle
13	chr12:104444600-104449800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:104444600-104449800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:104444600-104451600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:104444600-104451600	Weak transcription	HMEC	breast
17	chr12:104444800-104449000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:104444800-104449400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:104444800-104452600	Weak transcription	Placenta	Placenta
20	chr12:104445000-104448800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:104448200-104449600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr12:104448400-104449000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:104448400-104449200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr12:104448400-104449200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr12:104448400-104449200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr12:104448400-104449200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr12:104448400-104449200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr12:104448400-104449200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:104448400-104449400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:104448400-104449600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:104448400-104449600	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr12:104448400-104450600	Enhancers	Fetal Muscle Leg	muscle
33	chr12:104448400-104450800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr12:104448600-104448800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:104448600-104448800	Enhancers	NHEK	skin
36	chr12:104448600-104449200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:104448600-104449600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:104448600-104449600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:104448600-104449800	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr12:104448600-104450200	Enhancers	Fetal Muscle Trunk	muscle

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