Variant report

Variant	rs10934122
Chromosome Location	chr3:111617861-111617862
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: 36 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10934118	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934123	0.91[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11922171	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12491508	0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12495997	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1282944	0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1282955	0.83[JPT][hapmap]
rs1282960	0.84[JPT][hapmap]
rs1282961	0.84[JPT][hapmap]
rs13064071	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13065448	0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1500045	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1500046	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1587455	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16858868	0.84[ASN][1000 genomes]
rs3749297	0.83[JPT][hapmap]
rs4608659	0.89[ASN][1000 genomes]
rs60821969	0.89[ASN][1000 genomes]
rs62277591	0.88[ASN][1000 genomes]
rs62277592	0.89[ASN][1000 genomes]
rs6438021	0.84[JPT][hapmap]
rs6767186	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6775272	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6781879	0.83[MEX][hapmap]
rs6784285	0.86[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6785402	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6785554	0.89[ASN][1000 genomes]
rs6789911	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6796290	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802150	0.89[ASN][1000 genomes]
rs6805339	0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6805359	0.83[MEX][hapmap]
rs7621455	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7621473	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs968825	0.84[JPT][hapmap]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10934122	PHLDB2	cis	lymphoblastoid	seeQTL
rs10934122	PHLDB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 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	chr3:111604400-111618000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:111604400-111618200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:111604400-111620600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:111604400-111621600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:111604400-111622000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:111604400-111625600	Weak transcription	Fetal Intestine Large	intestine
12	chr3:111604400-111629400	Weak transcription	Ovary	ovary
13	chr3:111604400-111632200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:111604800-111621600	Weak transcription	NHLF	lung
15	chr3:111604800-111622000	Weak transcription	Adipose Nuclei	Adipose
16	chr3:111604800-111632000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:111605000-111620400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:111605000-111629800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:111606400-111618400	Weak transcription	Placenta	Placenta
20	chr3:111609200-111618600	Weak transcription	Hela-S3	cervix
21	chr3:111609400-111622400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:111609600-111623200	Weak transcription	Fetal Heart	heart
23	chr3:111609800-111623200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:111610000-111623200	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:111610200-111621600	Weak transcription	Left Ventricle	heart
26	chr3:111610200-111622200	Weak transcription	Lung	lung
27	chr3:111610200-111627400	Weak transcription	Aorta	Aorta
28	chr3:111611000-111622000	Weak transcription	Right Ventricle	heart
29	chr3:111612400-111620400	Weak transcription	NH-A	brain
30	chr3:111613800-111620000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:111614400-111618800	Strong transcription	NHEK	skin
32	chr3:111614600-111619800	Weak transcription	HUVEC	blood vessel
33	chr3:111615600-111619400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:111615600-111619400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:111615600-111619600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:111615600-111622000	Weak transcription	Fetal Stomach	stomach
37	chr3:111617000-111618800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr3:111617000-111619400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:111617200-111619200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:111617400-111618000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:111617400-111618200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:111617400-111618400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:111617400-111618800	ZNF genes & repeats	Fetal Muscle Leg	muscle
44	chr3:111617400-111619200	Strong transcription	Osteobl	bone
45	chr3:111617400-111619400	Strong transcription	HMEC	breast
46	chr3:111617400-111619600	Strong transcription	HSMM	muscle
47	chr3:111617400-111621200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:111617600-111618600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
49	chr3:111617600-111618600	Strong transcription	A549	lung
50	chr3:111617600-111622200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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