Variant report

Variant	rs11838539
Chromosome Location	chr13:48668018-48668019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48667865..48670263-chr13:48806295..48809101,2	MCF-7	breast:
2	chr13:48611722..48613362-chr13:48667186..48669052,2	K562	blood:
3	chr13:48667088..48669248-chr13:48807095..48809011,2	K562	blood:
4	chr13:48651976..48654376-chr13:48667767..48670618,2	K562	blood:

Variant related genes	Relation type
ENSG00000136146	Chromatin interaction
ENSG00000136143	Chromatin interaction
ENSG00000136156	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11148102	1.00[CHB][hapmap]
rs11841025	0.89[CHB][hapmap]
rs11841517	1.00[CHB][hapmap]
rs11842654	1.00[CHB][hapmap]
rs12427516	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12427964	0.82[EUR][1000 genomes]
rs12428055	0.86[EUR][1000 genomes]
rs12428098	1.00[CHB][hapmap]
rs12429099	0.82[EUR][1000 genomes]
rs12429348	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12429746	0.82[EUR][1000 genomes]
rs12429993	0.82[EUR][1000 genomes]
rs12431057	0.82[EUR][1000 genomes]
rs12431130	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584738	1.00[CHB][hapmap]
rs12585232	1.00[CHB][hapmap]
rs1410116	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1968029	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2094191	0.86[EUR][1000 genomes]
rs2148242	0.82[EUR][1000 genomes]
rs2182374	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2296572	1.00[CHB][hapmap]
rs2897496	0.82[EUR][1000 genomes]
rs35710390	0.86[EUR][1000 genomes]
rs3742108	1.00[CHB][hapmap]
rs3782979	0.90[CHB][hapmap]
rs4942741	0.99[ASN][1000 genomes]
rs57957392	0.86[EUR][1000 genomes]
rs58316588	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58634823	0.86[EUR][1000 genomes]
rs61585711	0.82[EUR][1000 genomes]
rs7336631	0.99[ASN][1000 genomes]
rs7982479	0.90[CHB][hapmap];0.92[ASN][1000 genomes]
rs7997347	0.89[CHB][hapmap];0.85[JPT][hapmap];0.99[ASN][1000 genomes]
rs9526440	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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 target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48652800-48668200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:48653000-48668200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:48653200-48668200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:48655400-48668200	Weak transcription	Aorta	Aorta
5	chr13:48659800-48668200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr13:48662400-48668200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr13:48664600-48668200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr13:48666000-48668200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr13:48666600-48668200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr13:48666600-48668200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr13:48666600-48668400	Enhancers	Spleen	Spleen
12	chr13:48666800-48668400	Enhancers	Primary B cells from peripheral blood	blood
13	chr13:48666800-48668400	Enhancers	Pancreas	Pancrea
14	chr13:48666800-48668600	Flanking Active TSS	Dnd41	blood
15	chr13:48666800-48669400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr13:48667000-48668400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr13:48667000-48668600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:48667000-48669400	Active TSS	K562	blood
19	chr13:48667200-48668200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr13:48667200-48668600	Flanking Active TSS	Hela-S3	cervix
21	chr13:48667400-48668200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr13:48667400-48668600	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr13:48667600-48668200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr13:48667600-48668200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr13:48667600-48668200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr13:48667600-48668200	Enhancers	Brain Angular Gyrus	brain
27	chr13:48667600-48668200	Enhancers	Brain Substantia Nigra	brain
28	chr13:48667600-48668200	Active TSS	Colonic Mucosa	Colon
29	chr13:48667600-48668200	Enhancers	Ovary	ovary
30	chr13:48667600-48668200	Flanking Active TSS	GM12878-XiMat	blood
31	chr13:48667600-48668400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:48667600-48668400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr13:48667600-48668400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr13:48667600-48668400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr13:48667600-48668400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr13:48667600-48668400	Flanking Active TSS	Fetal Brain Female	brain
37	chr13:48667600-48668600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr13:48667600-48668600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:48667600-48668600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr13:48667600-48668600	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr13:48667600-48668600	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr13:48667600-48668600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr13:48667600-48668600	Flanking Active TSS	HMEC	breast
44	chr13:48667600-48668600	Flanking Active TSS	NH-A	brain
45	chr13:48667600-48668600	Flanking Active TSS	Osteobl	bone
46	chr13:48667600-48668800	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr13:48667600-48668800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr13:48667600-48668800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:48667600-48668800	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr13:48667600-48668800	Flanking Active TSS	Fetal Thymus	thymus

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