Variant report

Variant	rs7142362
Chromosome Location	chr14:70416718-70416719
allele	G/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	chr14:70415707-70417120	Hela-S3	cervix:	n/a	n/a
2	GATA2	chr14:70416523-70416897	SH-SY5Y	brain:	n/a	n/a
3	POLR2A	chr14:70416549-70416881	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70415189..70417750-chr14:70418196..70420827,2	MCF-7	breast:
2	chr14:70412865..70415128-chr14:70415541..70417322,2	MCF-7	breast:

Variant related genes	Relation type
SMOC1	TF binding region
ENSG00000198732	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1007288	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10139510	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10140088	0.94[ASN][1000 genomes]
rs10141617	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10142998	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10143792	0.94[ASN][1000 genomes]
rs10150210	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10220692	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1037801	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1037802	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1040905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11848845	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11849125	0.94[ASN][1000 genomes]
rs11849133	0.94[ASN][1000 genomes]
rs12586293	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12589352	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12590177	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12881989	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12883649	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12885374	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12885763	0.92[ASN][1000 genomes]
rs12889706	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12897618	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1380430	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1380431	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1459700	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1547088	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1585374	0.93[ASN][1000 genomes]
rs1585375	0.92[ASN][1000 genomes]
rs170566	0.80[CHD][hapmap];0.92[GIH][hapmap]
rs17107501	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs186599	0.83[CHD][hapmap];0.85[GIH][hapmap]
rs1903200	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2035011	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs227448	0.83[CHD][hapmap];0.85[GIH][hapmap]
rs34833758	0.94[ASN][1000 genomes]
rs3742909	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6573918	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6573919	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs67295508	0.94[ASN][1000 genomes]
rs7145638	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7148145	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7149785	0.91[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7152091	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7157289	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[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];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7157956	0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8003166	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs8004069	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs8011726	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs927413	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs984036	0.94[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7142362	SMOC1	cis	parietal	SCAN
rs7142362	UPF0639	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70412400-70417200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr14:70413600-70418400	Weak transcription	Fetal Brain Female	brain
3	chr14:70414800-70437400	Strong transcription	Hela-S3	cervix
4	chr14:70415400-70434400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr14:70415600-70419600	Weak transcription	HepG2	liver
6	chr14:70415800-70417600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr14:70415800-70420000	Weak transcription	Fetal Muscle Leg	muscle
8	chr14:70415800-70444600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr14:70416000-70416800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:70416000-70418600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr14:70416000-70418800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:70416000-70422600	Weak transcription	Brain Substantia Nigra	brain
13	chr14:70416200-70418400	Weak transcription	Liver	Liver
14	chr14:70416200-70418600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:70416200-70418800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:70416200-70418800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:70416200-70418800	Weak transcription	Brain Anterior Caudate	brain
18	chr14:70416200-70421800	Weak transcription	Brain Hippocampus Middle	brain
19	chr14:70416600-70417400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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