Variant report

Variant	rs34487399
Chromosome Location	chr2:127975621-127975622
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:127973375..127977110-chr2:128049967..128052200,3	MCF-7	breast:
2	chr2:127957550..127959520-chr2:127975505..127977152,2	MCF-7	breast:
3	chr2:127961531..127964078-chr2:127974115..127976124,2	MCF-7	breast:
4	chr2:127974300..127976848-chr2:127983797..127985574,2	MCF-7	breast:
5	chr2:127972542..127975941-chr2:127982453..127985678,4	MCF-7	breast:
6	chr2:127975205..127977314-chr2:127992465..127995136,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ERCC3-1	chr2:127975143-127976209	ucscGeneNc_uc002too_1

No data

Variant related genes	Relation type
ENSG00000186684	Chromatin interaction
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10167294	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10928764	0.86[EUR][1000 genomes]
rs1143407	0.92[EUR][1000 genomes]
rs11684068	0.80[EUR][1000 genomes]
rs11899601	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12613252	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12613254	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12613413	0.91[EUR][1000 genomes]
rs12614320	0.92[EUR][1000 genomes]
rs12617858	0.92[EUR][1000 genomes]
rs12619391	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13017103	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13390029	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13403918	0.92[EUR][1000 genomes]
rs13409933	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13414676	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13429925	0.91[EUR][1000 genomes]
rs2134794	0.92[EUR][1000 genomes]
rs2139142	0.80[EUR][1000 genomes]
rs28807127	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34006114	0.80[EUR][1000 genomes]
rs34441363	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34601617	0.91[EUR][1000 genomes]
rs34703177	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738948	0.93[EUR][1000 genomes]
rs3893313	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150434	0.91[EUR][1000 genomes]
rs4150492	0.92[EUR][1000 genomes]
rs4150506	0.92[EUR][1000 genomes]
rs4150514	0.92[EUR][1000 genomes]
rs4300780	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4359587	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4528711	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4662721	0.86[EUR][1000 genomes]
rs4662724	0.80[EUR][1000 genomes]
rs58063879	0.92[EUR][1000 genomes]
rs59027829	0.85[EUR][1000 genomes]
rs6430937	0.91[EUR][1000 genomes]
rs6716392	0.86[EUR][1000 genomes]
rs6738811	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6747862	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752139	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67771362	0.80[EUR][1000 genomes]
rs9752366	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9923	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv961678	chr2:127961305-127979990	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3331416	chr2:127962771-127980988	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs34487399	AC068282.3	cis	Whole Blood	GTEx
rs34487399	AC068282.3	cis	Esophagus Mucosa	GTEx
rs34487399	AC068282.3	cis	Muscle Skeletal	GTEx
rs34487399	AC068282.3	cis	Nerve Tibial	GTEx
rs34487399	AC068282.3	cis	lung	GTEx
rs34487399	AC068282.3	cis	Artery Tibial	GTEx
rs34487399	AC068282.3	cis	Thyroid	GTEx
rs34487399	AC068282.3	cis	Esophagus Muscularis	GTEx
rs34487399	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs34487399	AC068282.3	cis	Heart Left Ventricle	GTEx
rs34487399	MAP3K2	cis	multi-tissue	Pritchard
rs34487399	AC068282.3	cis	Stomach	GTEx
rs34487399	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs34487399	AC068282.3	cis	Artery Aorta	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127956400-127975800	Weak transcription	Fetal Kidney	kidney
2	chr2:127973200-127975800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:127974600-127975800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:127974600-127976400	Flanking Active TSS	Hela-S3	cervix
5	chr2:127975000-127975800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
6	chr2:127975000-127976200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:127975000-127976200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr2:127975200-127975800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:127975200-127975800	Flanking Active TSS	A549	lung
10	chr2:127975200-127976400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:127975200-127977200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr2:127975400-127975800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
13	chr2:127975400-127976000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
14	chr2:127975400-127976000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
15	chr2:127975400-127976000	Flanking Active TSS	NH-A	brain
16	chr2:127975400-127976200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr2:127975400-127976200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:127975400-127976200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr2:127975400-127976200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:127975400-127976200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
21	chr2:127975400-127976200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:127975600-127975800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:127975600-127975800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:127975600-127975800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:127975600-127975800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:127975600-127975800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:127975600-127975800	Weak transcription	Esophagus	oesophagus
28	chr2:127975600-127975800	Enhancers	Osteobl	bone
29	chr2:127975600-127976000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:127975600-127976000	Enhancers	HMEC	breast
31	chr2:127975600-127976200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:127975600-127976200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr2:127975600-127976200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:127975600-127976200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:127975600-127976400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
36	chr2:127975600-127976400	Bivalent Enhancer	Placenta	Placenta
37	chr2:127975600-127976800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:127975600-127977000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:127975600-127977200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:127975600-127977800	Enhancers	Lung	lung
41	chr2:127975600-127978200	Active TSS	NHEK	skin
42	chr2:127975600-127979000	Active TSS	H9 Cell Line	embryonic stem cell

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