Variant report

Variant	rs10499462
Chromosome Location	chr7:14757723-14757724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:14757340..14758014-chr7:15344576..15345303,4	MCF-7	breast:
2	chr7:14757467..14758291-chr7:15055705..15056411,2	MCF-7	breast:
3	chr7:14757081..14758001-chr7:15054605..15056087,5	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10228891	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10259838	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10278975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11971649	0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs12533352	0.91[ASN][1000 genomes]
rs12536592	0.86[ASN][1000 genomes]
rs12537147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12539208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12540121	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12669997	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12699654	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12699655	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12699658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13231864	0.89[ASN][1000 genomes]
rs13237347	0.89[ASN][1000 genomes]
rs1357856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1357872	0.91[ASN][1000 genomes]
rs1404613	0.87[CHD][hapmap]
rs1525074	0.89[ASN][1000 genomes]
rs1525099	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs1568846	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1568847	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17168435	1.00[ASW][hapmap]
rs17606181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17668635	0.85[ASN][1000 genomes]
rs17668761	0.88[ASN][1000 genomes]
rs1830029	0.80[EUR][1000 genomes]
rs1997040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs34587189	0.91[ASN][1000 genomes]
rs35046572	0.86[ASN][1000 genomes]
rs35731392	0.91[ASN][1000 genomes]
rs4521664	0.87[CHD][hapmap];0.86[GIH][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4719417	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6461120	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6461121	0.91[ASN][1000 genomes]
rs6947566	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6954517	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6965637	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6966274	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7784799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7785767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9639212	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9639213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9784967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

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	nsv949033	chr7:14086106-14860323	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1031041	chr7:14624127-14999201	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv538741	chr7:14624127-14999201	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv887712	chr7:14717872-14829858	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10499462	AGR2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:14712800-14775200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr7:14755000-14757800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr7:14756600-14758000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr7:14756600-14758200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr7:14757000-14758000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr7:14757600-14757800	Enhancers	H9 Cell Line	embryonic stem cell
7	chr7:14757600-14757800	Enhancers	Rectal Smooth Muscle	rectum
8	chr7:14757600-14758000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:14757600-14758000	Flanking Active TSS	Liver	Liver
10	chr7:14757600-14758000	Enhancers	Brain Cingulate Gyrus	brain
11	chr7:14757600-14758000	Enhancers	Skeletal Muscle Male	skeletal muscle

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