Variant report

Variant	rs1159972
Chromosome Location	chr13:49676732-49676733
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	chr13:49660417..49663395-chr13:49676657..49679527,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11617719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11620305	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12429554	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17477129	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61950726	0.86[EUR][1000 genomes]
rs61950727	0.86[EUR][1000 genomes]
rs61950730	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7990472	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	20 gene(s)	inside rSNPs	diseases
5	nsv1035	chr13:49656225-49700371	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	esv1796840	chr13:49671215-49760666	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1159972	SNORA31	cis	cerebellum	SCAN
rs1159972	CAB39L	cis	cerebellum	SCAN
rs1159972	TRIM13	cis	cerebellum	SCAN
rs1159972	KCNRG	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49639600-49687200	Weak transcription	Pancreas	Pancrea
2	chr13:49640600-49683800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr13:49649400-49684200	Weak transcription	Right Ventricle	heart
4	chr13:49651800-49684000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr13:49651800-49684000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr13:49655600-49684200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr13:49657200-49692400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:49657400-49684000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr13:49657800-49683800	Weak transcription	Primary B cells from cord blood	blood
10	chr13:49660000-49683600	Weak transcription	Primary T cells from cord blood	blood
11	chr13:49664000-49684000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr13:49665200-49684000	Weak transcription	Fetal Stomach	stomach
13	chr13:49666200-49684200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr13:49666400-49682400	Weak transcription	Fetal Intestine Small	intestine
15	chr13:49671800-49683800	Weak transcription	Brain Anterior Caudate	brain
16	chr13:49671800-49684200	Weak transcription	Left Ventricle	heart
17	chr13:49672200-49684200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr13:49672400-49684200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:49672600-49682000	Weak transcription	Psoas Muscle	Psoas
20	chr13:49672600-49684000	Weak transcription	Ovary	ovary
21	chr13:49673200-49682400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr13:49673200-49683800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr13:49673200-49683800	Weak transcription	HepG2	liver
24	chr13:49673600-49677800	Weak transcription	Hela-S3	cervix
25	chr13:49673600-49681600	Weak transcription	HSMM	muscle
26	chr13:49673600-49681800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr13:49673600-49682000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:49673600-49682000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr13:49673600-49682200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:49673600-49683600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr13:49673600-49683800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr13:49673600-49683800	Weak transcription	GM12878-XiMat	blood
33	chr13:49673600-49684000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr13:49673600-49684000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr13:49673600-49684000	Weak transcription	HMEC	breast
36	chr13:49673600-49684000	Weak transcription	NH-A	brain
37	chr13:49673600-49684000	Weak transcription	NHLF	lung
38	chr13:49673600-49684000	Weak transcription	Osteobl	bone
39	chr13:49673600-49684200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:49673600-49684400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr13:49673800-49683800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr13:49674000-49683800	Weak transcription	HUVEC	blood vessel
43	chr13:49675600-49678000	Enhancers	Liver	Liver
44	chr13:49675800-49679000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr13:49676000-49676800	Weak transcription	Placenta	Placenta
46	chr13:49676200-49684200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr13:49676600-49684000	Weak transcription	Primary T cells fromperipheralblood	blood

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