Variant report

Variant	rs790938
Chromosome Location	chr13:50663384-50663385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50652169..50667024-chr13:50693268..50703943,57	K562	blood:
2	chr13:50646342..50650617-chr13:50662203..50666443,4	K562	blood:
3	chr13:50653006..50665770-chr13:50696335..50703879,43	K562	blood:
4	chr13:50654073..50663597-chr13:50696674..50702768,25	MCF-7	breast:
5	chr13:50661950..50663880-chr13:50702187..50703696,2	MCF-7	breast:
6	chr13:50652189..50666968-chr13:50693462..50701392,46	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1086510	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1149854	1.00[EUR][1000 genomes]
rs1149855	1.00[EUR][1000 genomes]
rs1149856	1.00[EUR][1000 genomes]
rs1241386	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2252794	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2472595	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2740536	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2760916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2760917	0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2762062	1.00[EUR][1000 genomes]
rs55929963	1.00[EUR][1000 genomes]
rs56277884	1.00[EUR][1000 genomes]
rs56285935	1.00[EUR][1000 genomes]
rs56794415	1.00[EUR][1000 genomes]
rs58214088	1.00[EUR][1000 genomes]
rs58364236	1.00[EUR][1000 genomes]
rs58438849	1.00[EUR][1000 genomes]
rs58450365	1.00[EUR][1000 genomes]
rs58521176	1.00[EUR][1000 genomes]
rs59563441	1.00[EUR][1000 genomes]
rs59609469	1.00[EUR][1000 genomes]
rs59729773	1.00[EUR][1000 genomes]
rs59951137	1.00[EUR][1000 genomes]
rs60016474	1.00[EUR][1000 genomes]
rs60154020	1.00[EUR][1000 genomes]
rs61384266	1.00[EUR][1000 genomes]
rs61495306	1.00[EUR][1000 genomes]
rs706607	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs706612	0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7321063	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7323645	1.00[EUR][1000 genomes]
rs7330228	1.00[EUR][1000 genomes]
rs7336462	1.00[EUR][1000 genomes]
rs73494087	1.00[EUR][1000 genomes]
rs73495815	1.00[EUR][1000 genomes]
rs73495825	1.00[EUR][1000 genomes]
rs73495852	1.00[EUR][1000 genomes]
rs73495865	1.00[EUR][1000 genomes]
rs73495869	1.00[EUR][1000 genomes]
rs73495873	1.00[EUR][1000 genomes]
rs73495880	1.00[EUR][1000 genomes]
rs73495885	1.00[EUR][1000 genomes]
rs73495888	1.00[EUR][1000 genomes]
rs73495900	1.00[EUR][1000 genomes]
rs73498015	1.00[EUR][1000 genomes]
rs73498022	1.00[EUR][1000 genomes]
rs73498030	1.00[EUR][1000 genomes]
rs73498061	1.00[EUR][1000 genomes]
rs74079205	1.00[EUR][1000 genomes]
rs790936	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs790946	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7981983	1.00[EUR][1000 genomes]
rs7992306	1.00[EUR][1000 genomes]
rs7996036	1.00[EUR][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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription 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	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50657200-50665000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:50657200-50673400	Weak transcription	Pancreas	Pancrea
3	chr13:50657400-50673400	Weak transcription	Left Ventricle	heart
4	chr13:50657400-50673400	Weak transcription	HSMM	muscle
5	chr13:50658000-50673400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:50658000-50697200	Weak transcription	HSMMtube	muscle
7	chr13:50658200-50665800	Weak transcription	Fetal Intestine Small	intestine
8	chr13:50658400-50665800	Weak transcription	Psoas Muscle	Psoas
9	chr13:50658400-50673400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr13:50658600-50673400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr13:50659200-50666000	Weak transcription	GM12878-XiMat	blood
12	chr13:50659400-50666000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr13:50659400-50666000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:50659600-50665000	Weak transcription	Brain Hippocampus Middle	brain
15	chr13:50659600-50665200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr13:50659600-50665800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr13:50659600-50665800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr13:50659600-50666000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr13:50659600-50672600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr13:50659600-50673000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr13:50659600-50673200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr13:50659800-50664800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr13:50659800-50664800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr13:50659800-50665000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr13:50659800-50665000	Weak transcription	Brain Germinal Matrix	brain
26	chr13:50659800-50665200	Weak transcription	Fetal Heart	heart
27	chr13:50659800-50665400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr13:50659800-50665600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr13:50659800-50666000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr13:50659800-50666200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr13:50659800-50666200	Weak transcription	Adipose Nuclei	Adipose
32	chr13:50659800-50666600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr13:50659800-50668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr13:50659800-50669000	Weak transcription	NHDF-Ad	bronchial
35	chr13:50659800-50670800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:50659800-50671200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:50659800-50671600	Weak transcription	HMEC	breast
38	chr13:50659800-50672200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr13:50659800-50672400	Weak transcription	A549	lung
40	chr13:50659800-50672600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr13:50659800-50672600	Weak transcription	Fetal Lung	lung
42	chr13:50659800-50672600	Weak transcription	Osteobl	bone
43	chr13:50659800-50673400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr13:50659800-50673400	Weak transcription	NH-A	brain
45	chr13:50659800-50681600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr13:50659800-50697200	Weak transcription	Hela-S3	cervix
47	chr13:50660000-50663800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr13:50660200-50673400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr13:50660600-50663600	Strong transcription	Fetal Thymus	thymus
50	chr13:50660800-50665600	Weak transcription	Monocytes-CD14+_RO01746	blood

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