Variant report

Variant	rs4237929
Chromosome Location	chr12:10712196-10712197
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	chr12:10392959..10394973-chr12:10709982..10712933,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EIF2S3L.1-1	chr12:10709642-10712295	NONHSAT026886

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10772314	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10772316	0.80[ASN][1000 genomes]
rs10845161	0.91[JPT][hapmap]
rs10845171	0.83[ASN][1000 genomes]
rs10845173	0.81[ASN][1000 genomes]
rs10845175	1.00[JPT][hapmap]
rs11053856	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11053857	0.95[JPT][hapmap]
rs11053859	0.80[ASN][1000 genomes]
rs11053861	0.83[ASN][1000 genomes]
rs11053865	0.80[ASN][1000 genomes]
rs11053868	0.83[ASN][1000 genomes]
rs11053871	0.80[ASN][1000 genomes]
rs11611202	1.00[JPT][hapmap]
rs12312462	0.83[ASN][1000 genomes]
rs12423957	1.00[JPT][hapmap]
rs2002156	0.81[ASN][1000 genomes]
rs2002157	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2125093	0.83[ASN][1000 genomes]
rs2125096	0.83[ASN][1000 genomes]
rs2417745	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2417746	0.86[JPT][hapmap]
rs2417903	0.87[EUR][1000 genomes]
rs2417904	0.87[EUR][1000 genomes]
rs2607883	0.85[JPT][hapmap]
rs2607888	0.86[JPT][hapmap]
rs2607891	0.81[JPT][hapmap]
rs2607892	0.81[JPT][hapmap]
rs2607895	0.81[JPT][hapmap]
rs2607896	0.81[ASN][1000 genomes]
rs2607898	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2682474	0.81[ASN][1000 genomes]
rs2682476	0.81[JPT][hapmap]
rs3816567	1.00[JPT][hapmap]
rs4076336	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4237928	0.81[ASN][1000 genomes]
rs4476009	0.81[ASN][1000 genomes]
rs4763547	0.81[ASN][1000 genomes]
rs4763548	0.81[ASN][1000 genomes]
rs4763552	0.81[ASN][1000 genomes]
rs4763555	0.80[ASN][1000 genomes]
rs58917785	0.80[ASN][1000 genomes]
rs6488305	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6488306	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7300053	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7302693	0.88[EUR][1000 genomes]
rs7305642	0.88[EUR][1000 genomes]
rs7315503	0.88[EUR][1000 genomes]
rs7358656	0.83[ASN][1000 genomes]
rs7488589	0.83[ASN][1000 genomes]
rs7953221	0.83[ASN][1000 genomes]
rs7971934	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7978850	1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898766	chr12:10537269-10722585	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv557459	chr12:10560591-10729821	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv898772	chr12:10622047-10722585	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv557479	chr12:10644663-10729821	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv898773	chr12:10660850-10722585	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv898774	chr12:10666025-10722585	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv898775	chr12:10668694-10735786	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1039120	chr12:10675930-10755446	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10707800-10713200	Enhancers	Dnd41	blood
2	chr12:10709200-10712200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr12:10709800-10712200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:10709800-10712200	Enhancers	Fetal Thymus	thymus
5	chr12:10709800-10713400	Enhancers	Thymus	Thymus
6	chr12:10710200-10714200	Enhancers	Primary hematopoietic stem cells	blood
7	chr12:10710600-10712200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr12:10710800-10712200	ZNF genes & repeats	GM12878-XiMat	blood
9	chr12:10710800-10724800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:10711200-10713400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr12:10711600-10712200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr12:10711600-10712400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:10711800-10712200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr12:10711800-10712200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:10711800-10712400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr12:10712000-10712200	Enhancers	Primary B cells from peripheral blood	blood

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