Variant report

Variant	rs7560701
Chromosome Location	chr2:114026882-114026883
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114026056..114028346-chr2:114029301..114030897,2	MCF-7	breast:
2	chr2:114023172..114025279-chr2:114025318..114027200,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-1	chr2:114023053-114034158	ENSG00000189223.9

Extended variants
information (count: 24 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10864912	0.83[MEX][hapmap]
rs11123173	0.87[ASN][1000 genomes]
rs12990456	0.88[ASN][1000 genomes]
rs13001920	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1374161	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1466018	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1491584	0.87[JPT][hapmap]
rs1491585	0.92[JPT][hapmap]
rs1491586	0.87[JPT][hapmap]
rs2121245	0.86[JPT][hapmap]
rs2863244	0.87[JPT][hapmap]
rs4142815	0.87[ASN][1000 genomes]
rs4848323	0.83[MEX][hapmap]
rs4849188	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542127	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6720637	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6726151	0.89[ASN][1000 genomes]
rs6734610	0.89[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.89[ASN][1000 genomes]
rs6753216	0.91[ASN][1000 genomes]
rs895418	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7560701	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs7560701	LOC654433	cis	parietal	SCAN
rs7560701	AC016683.6	cis	Esophagus Muscularis	GTEx
rs7560701	AC016683.6	cis	lung	GTEx
rs7560701	PAX8	cis	parietal	SCAN
rs7560701	PAX8	cis	Esophagus Mucosa	GTEx
rs7560701	AC016683.6	cis	Muscle Skeletal	GTEx
rs7560701	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs7560701	PAX8	cis	multi-tissue	Pritchard
rs7560701	DPP10	cis	cerebellum	SCAN
rs7560701	LOC654433	cis	cerebellum	SCAN
rs7560701	AC016683.6	cis	Nerve Tibial	GTEx
rs7560701	AC016683.6	cis	Artery Tibial	GTEx
rs7560701	PAX8	cis	Adipose Subcutaneous	GTEx
rs7560701	PAX8	cis	lymphoblastoid	seeQTL
rs7560701	AC016683.6	cis	Esophagus Mucosa	GTEx
rs7560701	AC016683.6	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113999600-114028400	Weak transcription	Ovary	ovary
2	chr2:114010200-114030400	Weak transcription	GM12878-XiMat	blood
3	chr2:114016200-114028000	Weak transcription	Fetal Brain Female	brain
4	chr2:114019400-114028200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:114020000-114027800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:114021200-114028200	Strong transcription	Duodenum Mucosa	Duodenum
7	chr2:114021600-114028200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:114022200-114027600	Genic enhancers	Fetal Kidney	kidney
9	chr2:114023000-114027200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:114023200-114039800	Weak transcription	Gastric	stomach
11	chr2:114023400-114027000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:114024000-114030000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:114024200-114029000	Weak transcription	Placenta	Placenta
14	chr2:114025000-114028200	Weak transcription	Fetal Thymus	thymus
15	chr2:114025400-114027800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:114025800-114027000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr2:114025800-114028600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:114026200-114027600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:114026400-114028600	Weak transcription	Primary T cells from cord blood	blood
20	chr2:114026600-114033400	Weak transcription	Lung	lung
21	chr2:114026600-114034400	Weak transcription	Pancreas	Pancrea

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