Variant report

Variant	rs12098902
Chromosome Location	chr11:102164508-102164509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:102164440-102164590	AG09319	gingival:	n/a	n/a
2	CTCF	chr11:102164440-102164590	HMEC	breast:	n/a	n/a
3	CTCF	chr11:102164460-102164610	AG10803	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:102164432..102164949-chr11:102187477..102188175,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243777	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10501998	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10501999	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11225201	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11225202	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11225203	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11600522	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11602147	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11606268	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12280343	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12576911	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12787745	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12789170	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12794196	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17763827	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17763887	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17769417	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17878708	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1894113	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894114	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1894115	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2408344	0.84[ASN][1000 genomes]
rs2511293	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511295	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2604526	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2604527	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2604533	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2846848	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2846849	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2846857	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2846858	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2852879	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2852880	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2852881	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2852882	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2852891	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3132831	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35612369	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58277500	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61893629	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7480738	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7924744	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7928663	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7931341	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7938790	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9665961	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv832251	chr11:102012295-102181744	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1043388	chr11:102017719-102172857	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv3514195	chr11:102118479-102348362	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	esv3514197	chr11:102118479-102348362	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong 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 miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12098902	BIRC3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102159200-102164600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:102159200-102164600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:102159200-102164600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:102159200-102165000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr11:102159200-102165800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:102159600-102164800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:102160400-102165800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:102160600-102165000	Weak transcription	NHEK	skin
9	chr11:102160800-102164600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr11:102160800-102165200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:102160800-102165200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:102161000-102164600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:102161000-102164800	Weak transcription	Fetal Lung	lung
14	chr11:102161000-102164800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:102161000-102165200	Weak transcription	HSMM	muscle
16	chr11:102161000-102171800	Weak transcription	Aorta	Aorta
17	chr11:102161600-102164600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:102161600-102165000	Weak transcription	Dnd41	blood
19	chr11:102162000-102171400	Weak transcription	Fetal Thymus	thymus
20	chr11:102163400-102165000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:102163400-102165000	Enhancers	HepG2	liver
22	chr11:102163800-102164600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr11:102164000-102164600	Enhancers	Primary B cells from peripheral blood	blood
24	chr11:102164000-102165200	Enhancers	Primary B cells from cord blood	blood
25	chr11:102164200-102164600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr11:102164200-102164600	Enhancers	Osteobl	bone
27	chr11:102164200-102165000	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr11:102164200-102165400	Enhancers	Primary T cells from cord blood	blood
29	chr11:102164200-102166200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr11:102164400-102164600	Active TSS	Primary T cells fromperipheralblood	blood
31	chr11:102164400-102164600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:102164400-102164800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr11:102164400-102164800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:102164400-102165000	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr11:102164400-102165000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:102164400-102165000	Active TSS	GM12878-XiMat	blood
37	chr11:102164400-102165200	Weak transcription	A549	lung
38	chr11:102164400-102166400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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