Variant report

Variant	rs2706228
Chromosome Location	chr13:51288236-51288237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNASEH2B-4	chr13:51287754-51289476	NONHSAT033865

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11839057	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1323886	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1853558	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1853559	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2492345	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2540523	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2540524	0.85[EUR][1000 genomes]
rs2615123	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2706229	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2706234	0.92[ASN][1000 genomes]
rs2706235	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2706239	0.93[ASN][1000 genomes]
rs2706241	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2706242	0.88[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2706244	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2706245	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2761840	0.92[ASN][1000 genomes]
rs2761841	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761842	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761844	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761845	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761846	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761847	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2761849	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2761850	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2761851	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2761852	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2761853	0.92[ASN][1000 genomes]
rs2761854	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761855	0.92[ASN][1000 genomes]
rs2812235	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812238	0.92[ASN][1000 genomes]
rs2812241	0.92[ASN][1000 genomes]
rs2812242	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812243	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2812244	0.92[ASN][1000 genomes]
rs2812246	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812247	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812249	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2812250	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7328949	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv2753864	chr13:51136699-51375199	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1037350	chr13:51272518-51447354	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv561643	chr13:51286083-51306330	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51269400-51296800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:51285000-51289400	Enhancers	Fetal Muscle Leg	muscle
3	chr13:51285000-51290000	Weak transcription	Brain Substantia Nigra	brain
4	chr13:51286200-51288600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr13:51286200-51290600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr13:51286400-51288800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr13:51286400-51288800	Enhancers	HSMM	muscle
8	chr13:51286600-51289000	Enhancers	HSMMtube	muscle
9	chr13:51286800-51288600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr13:51287000-51288600	Flanking Active TSS	Dnd41	blood
11	chr13:51287200-51288400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:51287200-51289000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:51287200-51289200	Enhancers	Fetal Thymus	thymus
14	chr13:51287400-51288400	Enhancers	NHDF-Ad	bronchial
15	chr13:51287600-51288800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr13:51287600-51289000	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr13:51287600-51289000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr13:51287600-51289600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr13:51287600-51290800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr13:51287800-51288400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr13:51287800-51288400	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr13:51287800-51288400	Active TSS	Rectal Smooth Muscle	rectum
23	chr13:51287800-51288400	Enhancers	NHLF	lung
24	chr13:51287800-51288600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:51287800-51288600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr13:51287800-51288600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr13:51287800-51288600	Enhancers	NHEK	skin
28	chr13:51287800-51288800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr13:51287800-51288800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr13:51287800-51289000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:51287800-51289000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr13:51287800-51289200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:51287800-51289200	Enhancers	HMEC	breast
34	chr13:51287800-51289800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr13:51287800-51290600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr13:51287800-51292000	Active TSS	Brain Hippocampus Middle	brain
37	chr13:51288000-51288400	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr13:51288000-51288400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr13:51288000-51288400	Weak transcription	Adipose Nuclei	Adipose
40	chr13:51288000-51288400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr13:51288000-51288400	Enhancers	Spleen	Spleen
42	chr13:51288000-51288400	Flanking Active TSS	GM12878-XiMat	blood
43	chr13:51288000-51288400	Strong transcription	HepG2	liver
44	chr13:51288000-51288400	Flanking Active TSS	Osteobl	bone
45	chr13:51288000-51288600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr13:51288000-51288600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr13:51288000-51288600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr13:51288000-51288600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr13:51288000-51288600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr13:51288000-51288600	Active TSS	Rectal Mucosa Donor 29	rectum

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