Variant report

Variant	rs11172314
Chromosome Location	chr12:58123111-58123112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58108037..58111841-chr12:58122870..58126206,3	K562	blood:
2	chr12:57856178..57857976-chr12:58122107..58124525,2	K562	blood:
3	chr12:58085694..58088995-chr12:58116929..58123534,7	MCF-7	breast:
4	chr12:57911913..57914667-chr12:58122854..58126849,5	K562	blood:
5	chr12:57984952..57986609-chr12:58120823..58123199,2	K562	blood:
6	chr12:58085407..58089363-chr12:58117669..58123604,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166987	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166908	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11172290	0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs11172302	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172305	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172310	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12296750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307841	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12318065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12422249	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12424011	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs184712	0.88[ASN][1000 genomes]
rs2239891	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277323	1.00[ASW][hapmap]
rs34854770	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3893002	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760169	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv1851618	chr12:58109302-58131947	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
7	nsv826383	chr12:58118080-58123647	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv899122	chr12:58118248-58137563	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11172314	DGKA	cis	parietal	SCAN
rs11172314	KRT81	cis	cerebellum	SCAN
rs11172314	KRT76	cis	parietal	SCAN
rs11172314	WIBG	cis	cerebellum	SCAN
rs11172314	HOXC8	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58115200-58123600	Weak transcription	GM12878-XiMat	blood
2	chr12:58115600-58124000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:58118400-58132000	Strong transcription	Primary T cells from cord blood	blood
4	chr12:58119200-58132000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:58119600-58130400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:58119600-58130400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:58119600-58131200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:58119600-58131400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:58119600-58132400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:58119600-58132800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:58119600-58133000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:58119800-58128000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:58119800-58128600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:58120000-58129000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:58120000-58131400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr12:58120200-58129000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:58120200-58130200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:58120400-58131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:58120400-58132400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:58120600-58129200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
21	chr12:58120800-58128800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:58120800-58129200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:58121000-58124000	Weak transcription	HSMMtube	muscle
24	chr12:58121000-58129200	Strong transcription	Primary B cells from cord blood	blood
25	chr12:58121200-58124200	Weak transcription	A549	lung
26	chr12:58121200-58126800	Weak transcription	Brain Angular Gyrus	brain
27	chr12:58121200-58128000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:58121400-58124800	Weak transcription	Liver	Liver
29	chr12:58121400-58125200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:58121400-58132800	Strong transcription	Thymus	Thymus
31	chr12:58121600-58123200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:58121600-58125400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:58121600-58126000	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:58121600-58126400	Weak transcription	Brain Anterior Caudate	brain
35	chr12:58121600-58130200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:58121800-58123800	Weak transcription	Esophagus	oesophagus
37	chr12:58121800-58124000	Weak transcription	NHLF	lung
38	chr12:58121800-58125000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:58121800-58125400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:58121800-58129400	Strong transcription	Spleen	Spleen
41	chr12:58121800-58130200	Weak transcription	Gastric	stomach
42	chr12:58121800-58132400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr12:58122000-58123400	Weak transcription	Dnd41	blood
44	chr12:58122000-58124400	Weak transcription	Right Ventricle	heart
45	chr12:58122000-58129400	Weak transcription	Lung	lung
46	chr12:58122200-58123200	Weak transcription	Fetal Brain Female	brain
47	chr12:58122400-58124000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:58122800-58124200	Strong transcription	Fetal Muscle Leg	muscle
49	chr12:58122800-58128400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:58123000-58129600	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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