Variant report

Variant	rs226372
Chromosome Location	chr12:9279598-9279599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9216174..9218577-chr12:9277293..9280144,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245105	Chromatin interaction
ENSG00000214851	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10771357	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10842914	0.82[CEU][hapmap]
rs10842923	0.81[CEU][hapmap]
rs10842928	0.94[CEU][hapmap]
rs10842969	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs113973	0.89[JPT][hapmap]
rs2114851	0.94[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226362	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226366	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226367	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs226370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs226374	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226375	0.85[EUR][1000 genomes]
rs226376	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs226377	0.85[EUR][1000 genomes]
rs226380	0.90[JPT][hapmap]
rs226382	0.89[JPT][hapmap]
rs226386	0.90[JPT][hapmap]
rs226387	0.90[JPT][hapmap]
rs226388	0.90[JPT][hapmap]
rs226389	1.00[JPT][hapmap]
rs226391	0.90[JPT][hapmap]
rs226408	0.90[JPT][hapmap]
rs3759276	0.94[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4882981	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6487633	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7297589	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7305636	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	esv3504674	chr12:9243858-9318016	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3502154	chr12:9243906-9317851	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3502155	chr12:9243906-9317851	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3504685	chr12:9243948-9317959	Strong transcription Weak transcription Enhancers ZNF genes & repeats 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	10 gene(s)	inside rSNPs	diseases
7	nsv527404	chr12:9250601-9435244	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
8	nsv976735	chr12:9274937-9303290	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs226372	RP11-22B23.1	cis	Whole Blood	GTEx
rs226372	GAPDH	cis	parietal	SCAN
rs226372	SCARNA10	cis	parietal	SCAN
rs226372	DUSP16	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9262800-9289000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:9269000-9280400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr12:9269000-9319200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:9269200-9280400	Weak transcription	Primary T cells from cord blood	blood
5	chr12:9269200-9281800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:9270200-9289000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:9271800-9280400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:9272000-9289000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:9272200-9280200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:9272200-9282400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:9275000-9287400	Weak transcription	Gastric	stomach
12	chr12:9277200-9281000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:9277400-9281000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:9277600-9280200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:9277600-9288800	Weak transcription	Right Atrium	heart
16	chr12:9277800-9280800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:9277800-9282000	Weak transcription	Spleen	Spleen
18	chr12:9278000-9279600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:9278000-9283800	Active TSS	Liver	Liver
20	chr12:9278800-9281600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:9279000-9279800	Enhancers	Fetal Lung	lung
22	chr12:9279000-9281600	Enhancers	HepG2	liver
23	chr12:9279400-9280800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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