Variant report

Variant	rs788166
Chromosome Location	chr2:172915489-172915490
allele	C/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172913443..172915901-chr2:172963690..172966629,2	MCF-7	breast:
2	chr2:172895941..172897535-chr2:172913713..172916052,2	K562	blood:
3	chr2:171785524..171787845-chr2:172913575..172916118,2	K562	blood:
4	chr2:172909379..172916271-chr2:172947539..172952263,13	K562	blood:
5	chr2:172903508..172905484-chr2:172912161..172915678,3	MCF-7	breast:
6	chr2:172863680..172867220-chr2:172914121..172918663,4	MCF-7	breast:
7	chr2:172915456..172917874-chr2:172919849..172921461,2	MCF-7	breast:
8	chr2:172915241..172921806-chr2:172947514..172951783,14	MCF-7	breast:
9	chr2:172914458..172918465-chr2:172959410..172965426,7	MCF-7	breast:
10	chr2:172914690..172917285-chr2:172958653..172961540,2	MCF-7	breast:
11	chr2:172901732..172906441-chr2:172911766..172917938,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172878	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000144355	Chromatin interaction
ENSG00000115806	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1008151	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12052246	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12989560	0.81[AMR][1000 genomes]
rs12991740	0.86[CEU][hapmap]
rs13015360	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13020884	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1965160	0.83[YRI][hapmap]
rs2129475	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34054371	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34737109	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62183819	0.81[AMR][1000 genomes]
rs6433323	0.85[CEU][hapmap]
rs6725971	0.88[EUR][1000 genomes]
rs788163	0.96[YRI][hapmap]
rs788170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs788171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs796839	0.92[EUR][1000 genomes];0.98[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	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv875412	chr2:172903124-172942448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs788166	AC068039.4	cis	Thyroid	GTEx
rs788166	AC068039.4	cis	Esophagus Muscularis	GTEx
rs788166	AC068039.4	cis	Muscle Skeletal	GTEx
rs788166	AC068039.4	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172907800-172916000	Weak transcription	Fetal Kidney	kidney
2	chr2:172911000-172930000	Weak transcription	Primary T cells from cord blood	blood
3	chr2:172911200-172915600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:172911200-172947200	Weak transcription	HSMM	muscle
5	chr2:172911400-172916400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:172911400-172916600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:172911400-172916800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:172912200-172916400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:172912200-172917000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:172913000-172917000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:172913200-172917000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:172913400-172917200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:172914000-172937000	Weak transcription	Pancreas	Pancrea
14	chr2:172914400-172916600	Enhancers	HepG2	liver
15	chr2:172914400-172916800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:172914800-172918000	Enhancers	K562	blood
17	chr2:172914800-172918600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:172915200-172917400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:172915400-172915600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:172915400-172915600	Enhancers	Brain Angular Gyrus	brain
21	chr2:172915400-172915800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links