Variant report

Variant	rs3742912
Chromosome Location	chr14:70498353-70498354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:70497570..70499518-chr14:70502839..70505709,2	MCF-7	breast:
2	chr14:70498095..70500229-chr14:70502609..70504593,3	K562	blood:
3	chr14:70278462..70280862-chr14:70497209..70499902,2	MCF-7	breast:
4	chr14:70494747..70496910-chr14:70498282..70501125,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1005543	0.82[CHB][hapmap]
rs1156443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1156446	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17107635	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17107637	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17107651	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1998334	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs227402	0.83[CHD][hapmap]
rs2281663	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs55784307	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56029860	0.96[ASN][1000 genomes]
rs60011612	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72728002	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72729803	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72729808	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8010305	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs8015491	0.81[CEU][hapmap]
rs8016522	0.82[CHB][hapmap];0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv832824	chr14:70320639-70511401	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv817638	chr14:70489680-70500973	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3742912	KIAA0247	cis	cerebellum	SCAN
rs3742912	ATP6V1D	cis	cerebellum	SCAN
rs3742912	ARG2	cis	cerebellum	SCAN
rs3742912	SMOC1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70476000-70500000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr14:70476200-70499000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:70485800-70498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:70486000-70500400	Weak transcription	Aorta	Aorta
5	chr14:70486400-70502800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr14:70487800-70498400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr14:70488000-70498600	Weak transcription	Gastric	stomach
8	chr14:70489000-70499200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:70490200-70499200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr14:70490600-70498600	Weak transcription	NHEK	skin
11	chr14:70491400-70498600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:70492200-70499400	Weak transcription	Brain Germinal Matrix	brain
13	chr14:70493800-70499000	Weak transcription	HepG2	liver
14	chr14:70494200-70499600	Weak transcription	Spleen	Spleen
15	chr14:70494200-70499800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr14:70494400-70500200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr14:70494400-70500400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr14:70494600-70498600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr14:70494600-70498800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr14:70495800-70498600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr14:70496800-70498600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr14:70496800-70501000	Weak transcription	Pancreas	Pancrea
23	chr14:70497000-70499400	Weak transcription	Brain Substantia Nigra	brain
24	chr14:70497200-70503000	Weak transcription	Liver	Liver
25	chr14:70497400-70508400	Weak transcription	Fetal Brain Female	brain
26	chr14:70497600-70499600	Genic enhancers	Hela-S3	cervix
27	chr14:70497800-70498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:70498200-70500200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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