Variant report

Variant	rs12569922
Chromosome Location	chr10:90105306-90105307
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	chr10:89619839..89624557-chr10:90105061..90108196,4	MCF-7	breast:
2	chr10:89621098..89623104-chr10:90102972..90105384,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171862	Chromatin interaction
ENSG00000227268	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10887807	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11202703	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11202705	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11202706	0.90[ASN][1000 genomes]
rs11202722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11202726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202731	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11202734	0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs11528433	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11598623	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12217988	0.85[JPT][hapmap]
rs12219687	0.82[ASN][1000 genomes]
rs12219831	0.86[JPT][hapmap];0.85[YRI][hapmap]
rs12220632	0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs12221213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12572813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1426617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1582223	0.86[ASN][1000 genomes]
rs1582224	0.93[JPT][hapmap]
rs1613409	0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1648512	0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1648523	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17111200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1774970	0.93[JPT][hapmap]
rs1774971	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2195013	0.89[ASN][1000 genomes]
rs2241515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3740279	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs3781201	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs55749454	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59513062	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7075138	0.87[ASN][1000 genomes]
rs7097606	0.85[JPT][hapmap]
rs74149704	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74149714	0.84[ASN][1000 genomes]
rs74149715	0.84[ASN][1000 genomes]
rs752709	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7919335	0.90[ASN][1000 genomes]
rs792224	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs792225	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs792227	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs792228	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs792229	0.85[ASN][1000 genomes]
rs792232	0.93[JPT][hapmap]
rs880793	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs880794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv551838	chr10:90058637-90137045	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12569922	TBC1D22A	cis	Cerebellum	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90102000-90106600	Weak transcription	Right Atrium	heart
2	chr10:90103400-90106600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:90103600-90105600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:90103800-90106200	Weak transcription	Stomach Mucosa	stomach
5	chr10:90103800-90107200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr10:90104000-90107800	Weak transcription	Adipose Nuclei	Adipose
7	chr10:90104000-90108000	Weak transcription	Ovary	ovary
8	chr10:90104200-90106400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:90104200-90106400	Weak transcription	Fetal Lung	lung
10	chr10:90104200-90107000	Weak transcription	HSMMtube	muscle
11	chr10:90104400-90106000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr10:90104400-90106000	Weak transcription	Liver	Liver
13	chr10:90104400-90109000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:90104600-90105400	Enhancers	Dnd41	blood
15	chr10:90104600-90107200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr10:90104600-90108200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr10:90104800-90105600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr10:90104800-90106800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr10:90104800-90108400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr10:90104800-90108800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr10:90104800-90108800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr10:90104800-90109200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr10:90105000-90105600	Enhancers	Primary T cells from cord blood	blood
24	chr10:90105000-90105800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr10:90105000-90106000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr10:90105000-90107800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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