Variant report

Variant	rs4237928
Chromosome Location	chr12:10711622-10711623
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	chr12:10484044..10484911-chr12:10711156..10712037,3	MCF-7	breast:
2	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: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10734838	0.83[ASN][1000 genomes]
rs10743910	0.83[ASN][1000 genomes]
rs10772298	0.84[AFR][1000 genomes]
rs10772312	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10772315	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10772316	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772317	0.83[ASN][1000 genomes]
rs10772319	0.83[ASN][1000 genomes]
rs10772321	0.83[ASN][1000 genomes]
rs10772323	0.83[ASN][1000 genomes]
rs10772324	0.83[ASN][1000 genomes]
rs10772325	0.83[ASN][1000 genomes]
rs10772326	0.83[ASN][1000 genomes]
rs10772327	0.83[ASN][1000 genomes]
rs10772329	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10845161	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10845163	0.83[ASN][1000 genomes]
rs10845164	0.84[ASN][1000 genomes]
rs10845165	0.85[ASN][1000 genomes]
rs10845166	0.83[ASN][1000 genomes]
rs10845172	0.83[ASN][1000 genomes]
rs10845174	0.82[ASN][1000 genomes]
rs10845175	0.84[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11053857	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11053859	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053865	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11053869	0.83[ASN][1000 genomes]
rs11053870	0.83[ASN][1000 genomes]
rs11053871	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11611202	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12423957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1915322	0.83[ASN][1000 genomes]
rs1915323	0.83[ASN][1000 genomes]
rs2002156	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2002157	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2125092	0.83[ASN][1000 genomes]
rs2125094	0.84[ASN][1000 genomes]
rs2125095	0.83[ASN][1000 genomes]
rs2168750	0.83[ASN][1000 genomes]
rs2417745	0.81[JPT][hapmap]
rs2417746	0.81[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2417747	0.85[ASN][1000 genomes]
rs2417748	0.84[ASN][1000 genomes]
rs2607883	0.85[JPT][hapmap]
rs2607888	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs2607891	0.81[JPT][hapmap]
rs2607892	0.81[JPT][hapmap]
rs2607895	0.81[JPT][hapmap]
rs2607898	0.80[JPT][hapmap]
rs2682476	0.81[JPT][hapmap]
rs28403396	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28701155	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816567	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3867478	0.83[ASN][1000 genomes]
rs3983544	0.83[ASN][1000 genomes]
rs3983545	0.83[ASN][1000 genomes]
rs3983546	0.83[ASN][1000 genomes]
rs3983547	0.82[ASN][1000 genomes]
rs4076336	0.81[ASN][1000 genomes]
rs4237929	0.81[ASN][1000 genomes]
rs4476009	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763528	0.83[ASN][1000 genomes]
rs4763531	0.83[ASN][1000 genomes]
rs4763532	0.83[ASN][1000 genomes]
rs4763547	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763548	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763550	0.84[ASN][1000 genomes]
rs4763551	0.84[ASN][1000 genomes]
rs4763553	0.84[ASN][1000 genomes]
rs4763555	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763559	0.83[ASN][1000 genomes]
rs55837119	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58917785	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60367665	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61913124	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6488306	0.85[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6488307	0.83[ASN][1000 genomes]
rs7134658	0.83[ASN][1000 genomes]
rs7134908	0.83[ASN][1000 genomes]
rs7136964	0.81[ASN][1000 genomes]
rs7137465	0.82[ASN][1000 genomes]
rs7306285	0.83[ASN][1000 genomes]
rs7306724	0.85[ASN][1000 genomes]
rs7311860	0.84[ASN][1000 genomes]
rs7955359	0.81[ASN][1000 genomes]
rs7965052	0.84[ASN][1000 genomes]
rs7978850	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7980411	0.83[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4237928	KLRC3	cis	parietal	SCAN
rs4237928	KLRC2	cis	cerebellum	SCAN
rs4237928	MAGOHB	cis	parietal	SCAN

Chromatin state (count:17 , 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	chr12:10709800-10711800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
4	chr12:10709800-10712200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:10709800-10712200	Enhancers	Fetal Thymus	thymus
6	chr12:10709800-10713400	Enhancers	Thymus	Thymus
7	chr12:10710000-10711800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:10710200-10714200	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:10710600-10712200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr12:10710800-10711800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:10710800-10712000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:10710800-10712200	ZNF genes & repeats	GM12878-XiMat	blood
13	chr12:10710800-10724800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:10711200-10711800	Enhancers	Primary T cells from cord blood	blood
15	chr12:10711200-10713400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr12:10711600-10712200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr12:10711600-10712400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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