Variant report

Variant	rs6734610
Chromosome Location	chr2:114017029-114017030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-1	chr2:114016841-114017161	ENSG00000189223
2	lnc-PSD4-1	chr2:114016841-114017161	ENSG00000189223
3	lnc-PSD4-1	chr2:114016841-114017161	ENSG00000189223
4	lnc-PSD4-1	chr2:114016841-114017161	ENSG00000189223.9
5	lnc-PSD4-1	chr2:114016841-114017161	ENSG00000189223.9

Extended variants
information (count: 23 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10864912	0.81[CEU][hapmap]
rs11123173	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12990456	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13001920	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13429413	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1374161	0.89[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs1374163	0.82[YRI][hapmap]
rs1446246	0.81[CEU][hapmap]
rs1466018	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1491584	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1491585	0.82[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1491586	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2863244	0.94[ASW][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4142815	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4849188	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6542127	0.82[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6720637	0.80[ASN][1000 genomes]
rs6726151	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6753216	0.82[ASN][1000 genomes]
rs7560701	0.89[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.89[ASN][1000 genomes]
rs895418	0.92[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv535895	chr2:114015492-114037018	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6734610	AC016683.6	cis	Whole Blood	GTEx
rs6734610	PAX8	cis	parietal	SCAN
rs6734610	AC016683.6	cis	lung	GTEx
rs6734610	PAX8	cis	Adipose Subcutaneous	GTEx
rs6734610	AC016683.6	cis	Esophagus Mucosa	GTEx
rs6734610	LOC654433	cis	cerebellum	SCAN
rs6734610	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs6734610	AC016683.6	cis	Artery Tibial	GTEx
rs6734610	AC016683.6	cis	Esophagus Muscularis	GTEx
rs6734610	PAX8	cis	Esophagus Mucosa	GTEx
rs6734610	PAX8	cis	lymphoblastoid	seeQTL
rs6734610	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs6734610	LOC654433	cis	parietal	SCAN
rs6734610	AC016683.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:113999600-114028400	Weak transcription	Ovary	ovary
3	chr2:114009800-114019000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:114010200-114030400	Weak transcription	GM12878-XiMat	blood
5	chr2:114010400-114022400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:114013200-114019600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:114013400-114017600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:114013400-114018200	Weak transcription	Fetal Kidney	kidney
9	chr2:114013600-114020000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:114013800-114019800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr2:114014000-114018400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:114015200-114018600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:114015200-114022400	Weak transcription	Fetal Thymus	thymus
14	chr2:114015200-114022800	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:114015400-114017200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:114015400-114018400	Weak transcription	Primary B cells from cord blood	blood
17	chr2:114015600-114017800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:114015600-114018200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:114015800-114018000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:114015800-114018200	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr2:114015800-114018400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:114015800-114023600	Weak transcription	HSMM	muscle
23	chr2:114016000-114017600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:114016000-114018200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:114016000-114018400	Strong transcription	Placenta	Placenta
26	chr2:114016000-114019200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:114016200-114018200	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:114016200-114018400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:114016200-114020400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:114016200-114022200	Weak transcription	Primary T cells from cord blood	blood
31	chr2:114016200-114023600	Weak transcription	HSMMtube	muscle
32	chr2:114016200-114028000	Weak transcription	Fetal Brain Female	brain
33	chr2:114016400-114017200	Strong transcription	Dnd41	blood
34	chr2:114016400-114017600	Strong transcription	Fetal Stomach	stomach
35	chr2:114016400-114019400	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr2:114016400-114026000	Weak transcription	Fetal Heart	heart
37	chr2:114016600-114017400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:114016800-114017600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:114016800-114017600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:114016800-114017600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:114016800-114018400	Strong transcription	Adipose Nuclei	Adipose
42	chr2:114016800-114019400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:114017000-114017200	ZNF genes & repeats	Lung	lung

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