Variant report

Variant	rs35006857
Chromosome Location	chr2:114026383-114026384
allele	C/T
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: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1021409	0.88[ASN][1000 genomes]
rs11685107	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11685421	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11691437	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471722	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12476331	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478795	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999288	0.88[ASN][1000 genomes]
rs13015130	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900216	1.00[ASN][1000 genomes]
rs4848321	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877202	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895416	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895417	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935365	0.87[AMR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35006857	PAX8	cis	lung	GTEx
rs35006857	AC016683.6	cis	lung	GTEx
rs35006857	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs35006857	AC016683.6	cis	Whole Blood	GTEx

Chromatin state (count:28 , 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	chr2:114019200-114026800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:114019400-114028200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:114020000-114027800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:114021200-114028200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr2:114021600-114028200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:114022200-114026400	Strong transcription	Primary T cells from cord blood	blood
10	chr2:114022200-114027600	Genic enhancers	Fetal Kidney	kidney
11	chr2:114023000-114026800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:114023000-114027200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:114023200-114026800	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:114023200-114039800	Weak transcription	Gastric	stomach
15	chr2:114023400-114027000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:114024000-114030000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:114024200-114026800	Enhancers	Fetal Muscle Leg	muscle
18	chr2:114024200-114029000	Weak transcription	Placenta	Placenta
19	chr2:114025000-114028200	Weak transcription	Fetal Thymus	thymus
20	chr2:114025400-114027800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:114025600-114026600	Enhancers	HSMMtube	muscle
22	chr2:114025800-114027000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr2:114025800-114028600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:114026000-114026600	ZNF genes & repeats	Lung	lung
25	chr2:114026000-114026800	Enhancers	Fetal Heart	heart
26	chr2:114026200-114026400	Enhancers	HSMM	muscle
27	chr2:114026200-114026600	Enhancers	Pancreas	Pancrea
28	chr2:114026200-114027600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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