Variant report

Variant	rs4258429
Chromosome Location	chr12:8635888-8635889
allele	A/G
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	SRF	chr12:8635744-8636002	GM12878	blood:	n/a	chr12:8635865-8635878 chr12:8635863-8635880 chr12:8635867-8635876 chr12:8635866-8635877 chr12:8635864-8635879 chr12:8635867-8635878 chr12:8635861-8635879 chr12:8635863-8635881 chr12:8635867-8635881 chr12:8635860-8635877 chr12:8635866-8635883 chr12:8635862-8635880 chr12:8635865-8635876
2	MAX	chr12:8635767-8635967	NB4	blood:	n/a	chr12:8635903-8635913
3	SRF	chr12:8635694-8636154	ECC-1	luminal epithelium:	n/a	chr12:8635865-8635878 chr12:8635863-8635880 chr12:8635867-8635876 chr12:8635866-8635877 chr12:8635864-8635879 chr12:8635867-8635878 chr12:8635861-8635879 chr12:8635863-8635881 chr12:8635867-8635881 chr12:8635860-8635877 chr12:8635866-8635883 chr12:8635862-8635880 chr12:8635865-8635876
4	SRF	chr12:8635609-8636039	ECC-1	luminal epithelium:	n/a	chr12:8635865-8635878 chr12:8635863-8635880 chr12:8635867-8635876 chr12:8635866-8635877 chr12:8635864-8635879 chr12:8635867-8635878 chr12:8635861-8635879 chr12:8635863-8635881 chr12:8635867-8635881 chr12:8635860-8635877 chr12:8635866-8635883 chr12:8635862-8635880 chr12:8635865-8635876
5	SRF	chr12:8635739-8635975	HepG2	liver:	n/a	chr12:8635865-8635878 chr12:8635863-8635880 chr12:8635867-8635876 chr12:8635866-8635877 chr12:8635864-8635879 chr12:8635867-8635878 chr12:8635861-8635879 chr12:8635863-8635881 chr12:8635867-8635881 chr12:8635860-8635877 chr12:8635866-8635883 chr12:8635862-8635880 chr12:8635865-8635876
6	SRF	chr12:8635740-8636004	GM12878	blood:	n/a	chr12:8635865-8635878 chr12:8635863-8635880 chr12:8635867-8635876 chr12:8635866-8635877 chr12:8635864-8635879 chr12:8635867-8635878 chr12:8635861-8635879 chr12:8635863-8635881 chr12:8635867-8635881 chr12:8635860-8635877 chr12:8635866-8635883 chr12:8635862-8635880 chr12:8635865-8635876
7	SRF	chr12:8635780-8635990	GM12878	blood:	n/a	chr12:8635865-8635878 chr12:8635863-8635880 chr12:8635867-8635876 chr12:8635866-8635877 chr12:8635864-8635879 chr12:8635867-8635878 chr12:8635861-8635879 chr12:8635863-8635881 chr12:8635867-8635881 chr12:8635860-8635877 chr12:8635866-8635883 chr12:8635862-8635880 chr12:8635865-8635876
8	POLR2A	chr12:8635858-8636165	A549	lung:	n/a	n/a
9	SRF	chr12:8635712-8635998	H1-hESC	embryonic stem cell:	n/a	chr12:8635865-8635878 chr12:8635863-8635880 chr12:8635867-8635876 chr12:8635866-8635877 chr12:8635864-8635879 chr12:8635867-8635878 chr12:8635861-8635879 chr12:8635863-8635881 chr12:8635867-8635881 chr12:8635860-8635877 chr12:8635866-8635883 chr12:8635862-8635880 chr12:8635865-8635876

Variant related genes	Relation type
RNU6-275P	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10734713	0.97[EUR][1000 genomes]
rs10770775	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10770776	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10770793	0.82[EUR][1000 genomes]
rs11045643	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11045652	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11045708	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11045757	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11045810	0.82[EUR][1000 genomes]
rs12302854	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12304190	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12308954	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12322968	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12423976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242889	0.98[EUR][1000 genomes]
rs4242891	0.95[EUR][1000 genomes]
rs4242892	0.97[EUR][1000 genomes]
rs4242893	0.98[EUR][1000 genomes]
rs4242895	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4268555	0.84[EUR][1000 genomes]
rs4303299	0.96[EUR][1000 genomes]
rs4334073	0.98[EUR][1000 genomes]
rs4427631	0.98[EUR][1000 genomes]
rs4445713	0.93[EUR][1000 genomes]
rs4447245	0.98[EUR][1000 genomes]
rs4457803	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460883	0.98[EUR][1000 genomes]
rs4477485	0.83[EUR][1000 genomes]
rs4882949	0.98[EUR][1000 genomes]
rs4882950	0.84[EUR][1000 genomes]
rs4882951	0.84[EUR][1000 genomes]
rs4883154	0.97[EUR][1000 genomes]
rs4883164	0.98[EUR][1000 genomes]
rs7132871	0.83[EUR][1000 genomes]
rs7134303	0.98[EUR][1000 genomes]
rs7302011	0.98[EUR][1000 genomes]
rs7309596	0.98[EUR][1000 genomes]
rs7311079	0.81[EUR][1000 genomes]
rs7312686	0.98[EUR][1000 genomes]
rs7312713	0.98[EUR][1000 genomes]
rs7315590	0.98[EUR][1000 genomes]
rs7315873	0.98[EUR][1000 genomes]
rs7962791	0.98[EUR][1000 genomes]
rs7963053	0.98[EUR][1000 genomes]
rs7964875	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7976692	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976958	0.98[EUR][1000 genomes]
rs7977465	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7978179	0.98[EUR][1000 genomes]
rs7978218	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040302	chr12:8245364-8695612	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541397	chr12:8245364-8695612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1044543	chr12:8449100-8792569	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1039504	chr12:8494944-8780137	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv557342	chr12:8599397-8774527	Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv933050	chr12:8602789-8775989	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv518772	chr12:8615809-8667579	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv518125	chr12:8615809-8671274	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1035270	chr12:8619562-8674062	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv933555	chr12:8627165-8775989	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv933639	chr12:8627243-8775989	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv600	chr12:8631646-8645560	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4258429	CLEC6A	cis	Whole Blood	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8628000-8638200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:8628400-8637400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:8634400-8636200	Enhancers	Fetal Thymus	thymus
4	chr12:8634400-8636600	Enhancers	Primary T cells from cord blood	blood
5	chr12:8635000-8636000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:8635400-8636000	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr12:8635400-8636000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:8635400-8636000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:8635400-8636200	Enhancers	Spleen	Spleen
10	chr12:8635400-8636400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
11	chr12:8635600-8636000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:8635600-8636000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr12:8635600-8636000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:8635600-8636000	Enhancers	Duodenum Mucosa	Duodenum
15	chr12:8635600-8636200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr12:8635600-8638200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:8635800-8636200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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