Variant report

Variant	rs6590805
Chromosome Location	chr11:100546036-100546037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:100544851..100548714-chr11:100549572..100552377,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10431107	0.80[ASN][1000 genomes]
rs10431108	0.83[ASN][1000 genomes]
rs10750593	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10791423	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs10895001	0.83[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10895003	0.87[ASN][1000 genomes]
rs10895004	0.85[ASN][1000 genomes]
rs10895005	0.88[ASN][1000 genomes]
rs10895009	0.80[ASN][1000 genomes]
rs11224372	0.85[ASN][1000 genomes]
rs11224403	0.80[ASN][1000 genomes]
rs1216743	0.87[ASN][1000 genomes]
rs12269905	0.88[ASN][1000 genomes]
rs12280935	0.85[CEU][hapmap]
rs12288075	0.88[ASN][1000 genomes]
rs1502284	0.81[ASN][1000 genomes]
rs1532710	0.83[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1587647	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs17095329	0.85[ASN][1000 genomes]
rs1847149	0.81[ASN][1000 genomes]
rs1847150	0.81[ASN][1000 genomes]
rs2055449	0.97[ASN][1000 genomes]
rs2055450	0.96[ASN][1000 genomes]
rs2134301	0.87[ASN][1000 genomes]
rs2298609	0.82[ASN][1000 genomes]
rs4312035	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs4753980	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4754692	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4754695	0.82[ASN][1000 genomes]
rs486023	0.87[CHB][hapmap]
rs492237	0.87[CHB][hapmap]
rs607562	0.87[CHB][hapmap]
rs653320	0.92[ASN][1000 genomes]
rs6590810	0.83[ASN][1000 genomes]
rs6590811	0.81[ASN][1000 genomes]
rs6590813	0.80[ASN][1000 genomes]
rs667575	0.87[CHB][hapmap]
rs670401	0.92[ASN][1000 genomes]
rs7106603	0.81[ASN][1000 genomes]
rs7928871	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7933402	0.85[ASN][1000 genomes]
rs7938194	0.88[ASN][1000 genomes]
rs7938601	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7942556	0.83[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053430	chr11:99888390-100629136	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1042067	chr11:99889697-100629136	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv556122	chr11:99893282-100585889	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1037689	chr11:99895378-100624599	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1040942	chr11:99895378-100629136	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1039852	chr11:99901695-100610533	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv541152	chr11:99901695-100610533	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1045190	chr11:99913193-100627395	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv541153	chr11:99913193-100627395	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv529454	chr11:99913394-100627255	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1043022	chr11:100387466-100610533	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv832246	chr11:100426725-100606957	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6590805	MMP13	cis	parietal	SCAN
rs6590805	ARHGAP42	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100535200-100547400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr11:100537200-100547400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr11:100537600-100547600	Weak transcription	K562	blood
4	chr11:100541400-100551800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:100542400-100547400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:100543600-100552200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:100545200-100546600	Enhancers	Liver	Liver
8	chr11:100546000-100546200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr11:100546000-100546400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:100546000-100546400	Enhancers	Fetal Lung	lung
11	chr11:100546000-100546600	Enhancers	Placenta	Placenta
12	chr11:100546000-100548400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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