Variant report

Variant	rs13085147
Chromosome Location	chr3:111451383-111451384
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHLDB2-1	chr3:111451308-111451550	NONHSAT091150

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

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10934102	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10934103	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13071304	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13090883	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17423699	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17424287	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34307743	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34444935	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35320181	0.87[AMR][1000 genomes]
rs3922703	1.00[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs3922705	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4234403	1.00[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs4234405	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4308247	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4349472	1.00[CEU][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs4373040	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4405880	0.92[EUR][1000 genomes]
rs4416359	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4429600	1.00[CEU][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4438630	0.92[EUR][1000 genomes]
rs4546124	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4642091	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs4645114	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4682058	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs4682059	0.80[CEU][hapmap];0.92[EUR][1000 genomes]
rs4682060	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs4682061	0.92[EUR][1000 genomes]
rs4682304	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs4682306	0.89[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs4682307	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs4682308	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs4682309	0.83[EUR][1000 genomes]
rs4682311	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4682315	0.90[EUR][1000 genomes]
rs6438005	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66499316	0.90[EUR][1000 genomes]
rs6762439	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6763624	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6768626	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6777990	0.90[EUR][1000 genomes]
rs6780845	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs6782894	1.00[CEU][hapmap]
rs6786443	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6791845	1.00[CEU][hapmap]
rs6804906	0.92[EUR][1000 genomes]
rs6807045	0.89[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs68097220	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7632963	0.92[EUR][1000 genomes]
rs7633037	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7637178	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs7640556	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7641533	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs9288929	0.92[EUR][1000 genomes]
rs9631450	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs9850851	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs9968124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
2	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:111431600-111451400	Weak transcription	Gastric	stomach
4	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
5	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:111442400-111456000	Weak transcription	Lung	lung
8	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
10	chr3:111443800-111451400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
12	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:111447200-111451800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:111448800-111453600	Weak transcription	Right Atrium	heart
15	chr3:111448800-111454200	Weak transcription	Adipose Nuclei	Adipose
16	chr3:111449000-111453400	Weak transcription	Fetal Heart	heart
17	chr3:111449000-111453600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:111449000-111453600	Weak transcription	HUVEC	blood vessel
19	chr3:111449000-111454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:111449000-111455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:111449200-111453600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:111449200-111453600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:111449400-111453400	Weak transcription	HSMMtube	muscle
24	chr3:111449400-111456000	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:111449600-111452600	Weak transcription	HSMM	muscle
26	chr3:111449600-111452800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:111449600-111452800	Weak transcription	Hela-S3	cervix
28	chr3:111449600-111452800	Weak transcription	Osteobl	bone
29	chr3:111449600-111453400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:111449600-111453400	Weak transcription	NH-A	brain
31	chr3:111449600-111453600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:111449600-111453800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:111449600-111453800	Weak transcription	NHLF	lung
34	chr3:111449600-111456000	Weak transcription	Esophagus	oesophagus
35	chr3:111449800-111453600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:111449800-111453600	Weak transcription	NHDF-Ad	bronchial
37	chr3:111450200-111452800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:111451000-111451400	Enhancers	Fetal Intestine Large	intestine
39	chr3:111451000-111451400	Enhancers	Fetal Intestine Small	intestine
40	chr3:111451000-111451400	Enhancers	Stomach Mucosa	stomach
41	chr3:111451000-111451400	Flanking Active TSS	A549	lung
42	chr3:111451000-111451400	Flanking Active TSS	HepG2	liver
43	chr3:111451000-111451600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr3:111451000-111453000	Active TSS	Fetal Kidney	kidney
45	chr3:111451200-111451400	Enhancers	Duodenum Mucosa	Duodenum
46	chr3:111451200-111451400	Enhancers	NHEK	skin
47	chr3:111451200-111451600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:111451200-111451600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:111451200-111451600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr3:111451200-111452000	Enhancers	HMEC	breast

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