Variant report

Variant	rs6796403
Chromosome Location	chr3:111619095-111619096
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLCXD2-2	chr3:111615806-111619675	NONHSAT091152

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1282951	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062225	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080181	1.00[ASN][1000 genomes]
rs13083727	0.87[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16858828	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16858904	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17492619	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2015457	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2137596	1.00[CHB][hapmap]
rs2137597	1.00[CHB][hapmap]
rs2272289	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584013	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34280973	1.00[ASN][1000 genomes]
rs34758094	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35058055	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35273140	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35398004	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35423545	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35475895	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35831430	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36133898	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4491869	1.00[CHB][hapmap]
rs4640528	1.00[CHB][hapmap]
rs56054847	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438023	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66515458	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802641	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71315891	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228590	1.00[ASN][1000 genomes]
rs7626033	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626336	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634410	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643903	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653069	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811962	0.87[ASN][1000 genomes]
rs9834691	1.00[ASN][1000 genomes]
rs9849340	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111585200-111622000	Weak transcription	HSMMtube	muscle
2	chr3:111591600-111633200	Weak transcription	Fetal Kidney	kidney
3	chr3:111601600-111620400	Weak transcription	Fetal Lung	lung
4	chr3:111601800-111620600	Weak transcription	NHDF-Ad	bronchial
5	chr3:111604000-111632200	Weak transcription	Gastric	stomach
6	chr3:111604400-111620600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:111604400-111621600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:111604400-111622000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:111604400-111625600	Weak transcription	Fetal Intestine Large	intestine
10	chr3:111604400-111629400	Weak transcription	Ovary	ovary
11	chr3:111604400-111632200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:111604800-111621600	Weak transcription	NHLF	lung
13	chr3:111604800-111622000	Weak transcription	Adipose Nuclei	Adipose
14	chr3:111604800-111632000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:111605000-111620400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:111605000-111629800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:111609400-111622400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:111609600-111623200	Weak transcription	Fetal Heart	heart
19	chr3:111609800-111623200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:111610000-111623200	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:111610200-111621600	Weak transcription	Left Ventricle	heart
22	chr3:111610200-111622200	Weak transcription	Lung	lung
23	chr3:111610200-111627400	Weak transcription	Aorta	Aorta
24	chr3:111611000-111622000	Weak transcription	Right Ventricle	heart
25	chr3:111612400-111620400	Weak transcription	NH-A	brain
26	chr3:111613800-111620000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:111614600-111619800	Weak transcription	HUVEC	blood vessel
28	chr3:111615600-111619400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:111615600-111619400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:111615600-111619600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:111615600-111622000	Weak transcription	Fetal Stomach	stomach
32	chr3:111617000-111619400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:111617200-111619200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:111617400-111619200	Strong transcription	Osteobl	bone
35	chr3:111617400-111619400	Strong transcription	HMEC	breast
36	chr3:111617400-111619600	Strong transcription	HSMM	muscle
37	chr3:111617400-111621200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:111617600-111622200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:111617600-111631800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:111617800-111623200	Weak transcription	Liver	Liver
41	chr3:111617800-111623400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:111618200-111628800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:111618400-111619400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:111618400-111623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:111618600-111619800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:111618600-111620000	Strong transcription	Hela-S3	cervix
47	chr3:111618600-111621600	Weak transcription	A549	lung
48	chr3:111618800-111620000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:111618800-111620000	Genic enhancers	NHEK	skin
50	chr3:111618800-111620800	Weak transcription	Placenta Amnion	Placenta Amnion

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