Variant report

Variant	rs3895894
Chromosome Location	chr12:42904578-42904579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1008040	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10785343	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10880309	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880311	0.94[ASN][1000 genomes]
rs12424992	0.97[ASN][1000 genomes]
rs12822031	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1985217	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2019557	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2406678	0.98[ASN][1000 genomes]
rs2406680	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[ASN][1000 genomes]
rs2406681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs2406682	0.97[ASN][1000 genomes]
rs28491015	0.98[ASN][1000 genomes]
rs28689646	0.94[ASN][1000 genomes]
rs4768414	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768415	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768416	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7307491	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9669495	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42878600-42904800	Weak transcription	Right Atrium	heart
2	chr12:42885400-42913600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:42886800-42904800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:42890600-42905800	Weak transcription	Osteobl	bone
5	chr12:42891000-42910200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:42898400-42914000	Weak transcription	NH-A	brain
7	chr12:42898400-42929000	Weak transcription	Fetal Kidney	kidney
8	chr12:42898600-42910400	Weak transcription	Fetal Stomach	stomach
9	chr12:42899000-42910000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:42901200-42905800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:42901400-42905200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:42901600-42904600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:42901600-42904600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:42901600-42940200	Weak transcription	Ovary	ovary
15	chr12:42902600-42904800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:42903000-42904600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:42903000-42913400	Weak transcription	HMEC	breast
18	chr12:42903200-42905000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:42903400-42904600	Weak transcription	Fetal Heart	heart
20	chr12:42903400-42904800	Weak transcription	Left Ventricle	heart
21	chr12:42903400-42905000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:42903400-42917800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:42903400-42917800	Weak transcription	HSMMtube	muscle
24	chr12:42904000-42910400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:42904400-42905000	Strong transcription	HUVEC	blood vessel
26	chr12:42904400-42905200	Enhancers	H9 Cell Line	embryonic stem cell
27	chr12:42904400-42905400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr12:42904400-42905600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr12:42904400-42906000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr12:42904400-42906200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr12:42904400-42906600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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