Variant report

Variant	rs1007288
Chromosome Location	chr14:70410483-70410484
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70382423..70384132-chr14:70408003..70410607,2	MCF-7	breast:
2	chr14:70403462..70405160-chr14:70409353..70411324,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10139510	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10140088	0.96[ASN][1000 genomes]
rs10141617	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10142998	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs10143792	0.96[ASN][1000 genomes]
rs10150210	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10220692	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1037801	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1037802	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1040905	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11848845	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11849125	0.96[ASN][1000 genomes]
rs11849133	0.96[ASN][1000 genomes]
rs12586293	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12589352	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12590177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12881989	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12883649	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12885374	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12885763	0.94[ASN][1000 genomes]
rs12889706	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12897618	0.97[ASN][1000 genomes]
rs1380430	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1380431	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1459700	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1547088	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1585374	0.95[ASN][1000 genomes]
rs1585375	0.94[ASN][1000 genomes]
rs170566	0.84[CHD][hapmap];0.85[GIH][hapmap]
rs17107501	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs186599	0.82[CHD][hapmap]
rs1903200	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2035011	1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs227448	0.82[CHD][hapmap]
rs34833758	0.96[ASN][1000 genomes]
rs3742909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6573918	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6573919	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs67295508	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7142362	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7145638	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7148145	0.99[ASN][1000 genomes]
rs7149785	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7152091	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7157289	1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7157956	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs8003166	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs8004069	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs8011726	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs927413	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs984036	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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
rs1007288	SMOC1	cis	parietal	SCAN
rs1007288	GALNTL1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70403600-70411600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:70405200-70410800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr14:70407800-70411200	Enhancers	Pancreas	Pancrea
4	chr14:70408400-70410800	Enhancers	Fetal Intestine Large	intestine
5	chr14:70408800-70410800	Enhancers	Fetal Intestine Small	intestine
6	chr14:70409000-70410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr14:70409000-70410600	Strong transcription	Hela-S3	cervix
8	chr14:70409400-70410800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr14:70409400-70411000	Enhancers	Gastric	stomach
10	chr14:70409600-70410600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr14:70409800-70413200	Enhancers	Liver	Liver
12	chr14:70410000-70410800	Enhancers	Fetal Muscle Leg	muscle
13	chr14:70410000-70415800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:70410200-70410600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:70410400-70410600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:70410400-70410600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:70410400-70410800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:70410400-70411400	Enhancers	HepG2	liver

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