Variant report

Variant	rs2286657
Chromosome Location	chr13:51087007-51087008
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:51085819..51089100-chr13:51090794..51093089,4	K562	blood:
2	chr13:51066276..51068266-chr13:51086109..51088000,2	K562	blood:
3	chr13:50569721..50571547-chr13:51085881..51088680,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNASEH2B-3	chr13:51086748-51087029	NONHSAT033861

Variant related genes	Relation type
ENSG00000204977	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000176124	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs279075	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4603449	0.83[AFR][1000 genomes]
rs61962260	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6561582	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7983949	0.88[CHB][hapmap]
rs7991128	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7994628	0.94[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9316500	0.91[ASN][1000 genomes]
rs9562984	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9562985	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562986	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568434	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568440	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568441	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568442	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9634835	0.82[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs963740	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1045237	chr13:50976560-51102386	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1040	chr13:51041591-51090903	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1835159	chr13:51061044-51091390	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1815534	chr13:51061044-51092946	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1816672	chr13:51061044-51092946	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv1830736	chr13:51061044-51092946	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv1834352	chr13:51061044-51092946	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv1841390	chr13:51061044-51092946	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv1843375	chr13:51061044-51092946	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51084200-51093200	Weak transcription	Spleen	Spleen
2	chr13:51084400-51093000	Weak transcription	Lung	lung
3	chr13:51085400-51087800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:51085600-51089200	Enhancers	Fetal Intestine Small	intestine
5	chr13:51085800-51087600	Flanking Active TSS	Dnd41	blood
6	chr13:51086000-51087200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr13:51086000-51087200	Flanking Active TSS	Fetal Lung	lung
8	chr13:51086000-51087200	Flanking Active TSS	GM12878-XiMat	blood
9	chr13:51086000-51087400	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr13:51086000-51087400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr13:51086000-51087400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr13:51086000-51087600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr13:51086000-51088000	Enhancers	Fetal Kidney	kidney
14	chr13:51086000-51088000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr13:51086000-51088200	Enhancers	Fetal Stomach	stomach
16	chr13:51086200-51087200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr13:51086200-51087200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr13:51086200-51087200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr13:51086200-51087200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr13:51086200-51087200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:51086200-51087200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr13:51086200-51087200	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr13:51086200-51087200	Flanking Active TSS	Thymus	Thymus
24	chr13:51086200-51087400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr13:51086200-51087400	Flanking Active TSS	Osteobl	bone
26	chr13:51086200-51087600	Enhancers	Small Intestine	intestine
27	chr13:51086200-51093000	Weak transcription	Placenta	Placenta
28	chr13:51086400-51087200	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr13:51086400-51087200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr13:51086400-51087200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr13:51086400-51087200	Active TSS	Brain Anterior Caudate	brain
32	chr13:51086400-51087200	Active TSS	Brain Hippocampus Middle	brain
33	chr13:51086400-51087200	Active TSS	Colonic Mucosa	Colon
34	chr13:51086400-51087200	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr13:51086400-51087200	Active TSS	Right Atrium	heart
36	chr13:51086400-51087400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:51086400-51087400	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr13:51086400-51087400	Flanking Active TSS	Liver	Liver
39	chr13:51086400-51087400	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr13:51086400-51087600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr13:51086400-51087600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr13:51086400-51092400	Weak transcription	Pancreas	Pancrea
43	chr13:51086600-51087200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr13:51086600-51087200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr13:51086600-51087200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr13:51086600-51087200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr13:51086600-51087200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr13:51086600-51087200	Active TSS	Brain Angular Gyrus	brain
49	chr13:51086600-51087200	Active TSS	Brain Germinal Matrix	brain
50	chr13:51086600-51087200	Active TSS	Brain Substantia Nigra	brain

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