Variant report

Variant	rs2120066
Chromosome Location	chr13:76450134-76450135
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr13:76450079-76451484	SK-N-SH	brain:	n/a	chr13:76450402-76450412 chr13:76450400-76450413 chr13:76451175-76451187 chr13:76450711-76450730

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76450119..76450751-chr13:76590749..76591620,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223458	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1015694	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1036867	0.81[ASN][1000 genomes]
rs1036868	0.81[ASN][1000 genomes]
rs10507835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1323565	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1323566	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1323567	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1323568	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1397	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1399	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1400	0.81[JPT][hapmap]
rs1550620	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4572275	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs4884024	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4885358	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885362	0.81[ASN][1000 genomes]
rs6562923	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7981821	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7986419	0.84[ASN][1000 genomes]
rs7986876	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9318381	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs9530475	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs9530477	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9530483	0.81[ASN][1000 genomes]
rs9530484	0.81[ASN][1000 genomes]
rs9544060	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9544071	0.81[ASN][1000 genomes]
rs9600572	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9600574	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9600575	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9600577	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9600578	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9600579	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9600581	0.81[ASN][1000 genomes]
rs9600582	0.81[ASN][1000 genomes]
rs969394	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[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	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv832649	chr13:76424872-76657891	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2120066	RP11-173B14.5	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76440000-76469200	Weak transcription	HSMM	muscle
2	chr13:76444400-76451000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr13:76444800-76450400	Weak transcription	Fetal Heart	heart
4	chr13:76445000-76450200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr13:76445000-76450200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:76445000-76450400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:76445000-76450400	Weak transcription	Fetal Intestine Small	intestine
8	chr13:76445000-76450400	Weak transcription	GM12878-XiMat	blood
9	chr13:76445000-76450600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr13:76445000-76450800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:76445000-76451000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr13:76445200-76450200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr13:76445200-76450400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr13:76445200-76451000	Weak transcription	Colon Smooth Muscle	Colon
15	chr13:76445400-76450400	Weak transcription	A549	lung
16	chr13:76445400-76454400	Weak transcription	Osteobl	bone
17	chr13:76445600-76450400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:76445600-76450400	Weak transcription	Fetal Brain Female	brain
19	chr13:76445600-76453400	Weak transcription	Adipose Nuclei	Adipose
20	chr13:76445600-76453600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr13:76446000-76450400	Weak transcription	Fetal Muscle Leg	muscle
22	chr13:76448400-76450400	Weak transcription	HMEC	breast
23	chr13:76449000-76451000	Enhancers	Primary T cells from cord blood	blood
24	chr13:76449000-76451200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr13:76449000-76451600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr13:76449200-76450400	Weak transcription	Fetal Lung	lung
27	chr13:76449200-76451000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:76449400-76450400	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr13:76449600-76450400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr13:76449600-76450400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr13:76449600-76450600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr13:76449600-76450600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr13:76449600-76451600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr13:76449800-76450600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr13:76449800-76450800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr13:76449800-76450800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr13:76449800-76451000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr13:76449800-76451200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr13:76449800-76451200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr13:76450000-76450400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr13:76450000-76451200	Enhancers	Fetal Brain Male	brain
42	chr13:76450000-76451200	Enhancers	Fetal Thymus	thymus

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