Variant report

Variant	rs11172848
Chromosome Location	chr12:40007956-40007957
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40005732..40008128-chr12:40008934..40010953,2	K562	blood:
2	chr12:40006374..40007995-chr12:40011197..40013165,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10877173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877201	0.90[JPT][hapmap]
rs11172144	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11172162	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs11172480	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172616	0.86[ASN][1000 genomes]
rs11172645	0.86[ASN][1000 genomes]
rs11172646	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172647	0.86[ASN][1000 genomes]
rs11172687	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11172692	0.86[ASN][1000 genomes]
rs11172697	0.86[ASN][1000 genomes]
rs11172713	0.90[JPT][hapmap]
rs11172722	0.90[JPT][hapmap]
rs11172794	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11172896	0.91[ASN][1000 genomes]
rs11172897	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12227286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12227668	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12228013	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12228617	0.90[JPT][hapmap]
rs12229370	0.83[ASN][1000 genomes]
rs12230055	0.83[ASN][1000 genomes]
rs17127129	1.00[JPT][hapmap]
rs17127138	1.00[JPT][hapmap]
rs35790935	0.83[ASN][1000 genomes]
rs35858791	0.83[ASN][1000 genomes]
rs4072006	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4294600	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4298947	0.85[ASN][1000 genomes]
rs57847223	0.86[ASN][1000 genomes]
rs58036566	0.86[ASN][1000 genomes]
rs59518553	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59528535	0.91[ASN][1000 genomes]
rs6581228	0.90[JPT][hapmap]
rs7133376	0.90[JPT][hapmap]
rs7133599	0.86[ASN][1000 genomes]
rs7309234	0.92[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7310178	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7310871	0.86[ASN][1000 genomes]
rs7312611	0.90[JPT][hapmap]
rs73268358	0.91[ASN][1000 genomes]
rs73268359	0.91[ASN][1000 genomes]
rs7980857	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9668500	1.00[AMR][1000 genomes];0.98[EUR][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	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS 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 miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1039645	chr12:39903123-40022029	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv469359	chr12:39946354-40034699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv558591	chr12:39946354-40034699	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv469361	chr12:39946354-40042220	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv558592	chr12:39946354-40042220	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv899014	chr12:39946354-40068896	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak 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	2 gene(s)	inside rSNPs	diseases
10	nsv899015	chr12:39946354-40118249	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv899017	chr12:39949147-40081619	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv899018	chr12:39949147-40111761	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv899020	chr12:39985206-40040331	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv899021	chr12:39989172-40053423	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11172848	ABCD2	cis	multi-tissue	Pritchard
rs11172848	CXCL11	trans	brain	seeQTL
rs11172848	SOD2	trans	brain	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39963800-40010200	Weak transcription	Left Ventricle	heart
2	chr12:39966800-40009400	Weak transcription	Primary T cells from cord blood	blood
3	chr12:39980200-40009200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:39996800-40009400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:39999600-40009800	Weak transcription	Brain Anterior Caudate	brain
6	chr12:40000200-40009400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:40000200-40010200	Weak transcription	Brain Substantia Nigra	brain
8	chr12:40001200-40010000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:40002000-40009800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr12:40004400-40009200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr12:40005000-40012200	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:40005600-40008600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:40006000-40008200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr12:40006800-40009400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:40006800-40015000	Active TSS	GM12878-XiMat	blood
16	chr12:40007200-40008000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:40007400-40008000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr12:40007600-40008600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:40007600-40008600	Active TSS	Fetal Brain Female	brain
20	chr12:40007600-40012400	Active TSS	Adipose Nuclei	Adipose
21	chr12:40007800-40008000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:40007800-40008000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:40007800-40008000	Enhancers	Fetal Brain Male	brain
24	chr12:40007800-40008200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr12:40007800-40008200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr12:40007800-40008400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:40007800-40008400	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr12:40007800-40008400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:40007800-40008800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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