Variant report

Variant	rs2273986
Chromosome Location	chr12:10150974-10150975
allele	C/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	CTCF	chr12:10150927-10151011	MCF-7	breast:	n/a	n/a
2	CTCF	chr12:10150912-10151036	MCF-7	breast:	n/a	n/a
3	CTCF	chr12:10150917-10151039	GM12892	blood:	n/a	n/a
4	CTCF	chr12:10150938-10151046	GM19238	blood:	n/a	n/a
5	CTCF	chr12:10150955-10151019	NHEK	skin:	n/a	n/a
6	CTCF	chr12:10150866-10150997	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr12:10150933-10151026	MCF-7	breast:	n/a	n/a
8	CTCF	chr12:10150934-10151038	A549	lung:	n/a	n/a
9	POLR2A	chr12:10150877-10151021	A549	lung:	n/a	n/a
10	CTCF	chr12:10150942-10151028	GM12878	blood:	n/a	n/a
11	CTCF	chr12:10150944-10151010	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr12:10150935-10151031	MCF-7	breast:	n/a	n/a
13	CTCF	chr12:10150920-10151045	GM19239	blood:	n/a	n/a
14	CTCF	chr12:10150957-10151045	Kidney_OC	kidney:	n/a	n/a
15	CTCF	chr12:10150945-10151001	GM19240	blood:	n/a	n/a
16	CTCF	chr12:10150959-10150985	MCF-7	breast:	n/a	n/a
17	CTCF	chr12:10150964-10150997	Gliobla	brain:	n/a	n/a

Variant related genes	Relation type
CLEC1B	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10400564	0.83[YRI][hapmap]
rs1746123	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760953	0.87[EUR][1000 genomes]
rs2922161	0.85[EUR][1000 genomes]
rs2961542	0.87[EUR][1000 genomes]
rs2984956	0.87[EUR][1000 genomes]
rs3818341	0.81[ASN][1000 genomes]
rs4764178	0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4764179	0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4764180	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4764181	0.82[ASN][1000 genomes]
rs476564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs477751	0.85[EUR][1000 genomes]
rs478829	0.85[EUR][1000 genomes]
rs479624	0.85[EUR][1000 genomes]
rs483576	0.85[EUR][1000 genomes]
rs525013	0.87[EUR][1000 genomes]
rs526157	0.87[EUR][1000 genomes]
rs531425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs542700	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562627	0.87[EUR][1000 genomes]
rs562839	0.87[EUR][1000 genomes]
rs566505	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs581949	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs582968	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs611819	0.85[EUR][1000 genomes]
rs611821	0.85[EUR][1000 genomes]
rs612227	0.85[EUR][1000 genomes]
rs612270	0.83[EUR][1000 genomes]
rs613871	0.96[ASN][1000 genomes]
rs617956	0.96[ASN][1000 genomes]
rs640817	0.87[EUR][1000 genomes]
rs643003	0.87[EUR][1000 genomes]
rs7137254	0.85[EUR][1000 genomes]
rs7953702	0.85[EUR][1000 genomes]
rs7953814	0.84[EUR][1000 genomes]
rs7960084	0.82[YRI][hapmap]
rs7977955	0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977964	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980924	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935538	0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043125	chr12:10121288-10177037	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1042106	chr12:10121288-10177636	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1040610	chr12:10121288-10179374	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525593	chr12:10121347-10156646	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv898756	chr12:10142538-10174314	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv604	chr12:10144039-10160440	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2273986	RP11-133L14.5	cis	Whole Blood	GTEx
rs2273986	CLEC12B	cis	Whole Blood	GTEx
rs2273986	CLEC12A	cis	Whole Blood	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10145200-10155400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr12:10145200-10155800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:10145800-10153400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:10149800-10153400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:10150000-10153200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:10150800-10151800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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