Variant report

Variant	rs1388171
Chromosome Location	chr11:107143137-107143138
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10454489	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046094	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap]
rs1046095	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs10502087	0.95[CEU][hapmap];0.93[JPT][hapmap]
rs10749890	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749891	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10749896	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs10749903	0.84[CEU][hapmap]
rs10789592	0.86[ASN][1000 genomes]
rs10789593	0.85[ASN][1000 genomes]
rs10789615	0.81[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap]
rs10789616	0.91[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10789617	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs10789618	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap]
rs10789620	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs10789621	0.91[CEU][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap]
rs10890676	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10890680	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10890684	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890689	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890690	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890692	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890708	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs10890712	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs10890719	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs10890720	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs10890721	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11212111	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11212112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212114	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212116	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212117	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212166	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs11212182	0.95[CEU][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap]
rs11212197	0.90[CEU][hapmap];0.93[JPT][hapmap]
rs11212206	0.91[CEU][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap]
rs11212207	0.93[JPT][hapmap]
rs11602033	0.85[CEU][hapmap];0.93[JPT][hapmap]
rs11602214	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12286915	0.93[JPT][hapmap]
rs12287772	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106875	0.91[CEU][hapmap];0.87[JPT][hapmap]
rs2216998	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2355840	0.82[ASN][1000 genomes]
rs3758911	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap]
rs4387327	0.82[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap]
rs588921	0.82[CEU][hapmap];0.93[JPT][hapmap]
rs590699	0.91[CEU][hapmap];0.93[JPT][hapmap]
rs6588965	0.83[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7131522	0.81[ASN][1000 genomes]
rs7358308	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7929345	0.82[ASN][1000 genomes]
rs999984	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531938	chr11:106760733-107156814	Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv898364	chr11:106944975-107285636	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv898365	chr11:106944975-107430300	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv898366	chr11:106944975-107433835	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv898367	chr11:106944975-107443420	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv898369	chr11:106958304-107443420	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv832260	chr11:106975094-107181795	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv556279	chr11:107006900-107186896	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1035911	chr11:107020991-107198181	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv898370	chr11:107027991-107430300	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1040190	chr11:107045534-107175661	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv898372	chr11:107049968-107433835	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1038368	chr11:107116577-107664181	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv541163	chr11:107116577-107664181	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	nsv898373	chr11:107124903-107433835	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1388171	MMP12	cis	cerebellum	SCAN
rs1388171	GRIA4	cis	cerebellum	SCAN
rs1388171	CWF19L2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107139400-107143800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:107140200-107146800	Weak transcription	Fetal Brain Male	brain
3	chr11:107141600-107143200	Enhancers	Stomach Mucosa	stomach

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