Variant report

Variant	rs12820641
Chromosome Location	chr12:9777100-9777101
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	CUX1	chr12:9776965-9777128	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNU6-700P	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10466762	0.89[ASN][1000 genomes]
rs10743776	0.89[ASN][1000 genomes]
rs10772005	0.89[ASN][1000 genomes]
rs10772006	0.89[ASN][1000 genomes]
rs10844236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844267	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844327	0.89[ASN][1000 genomes]
rs10844350	0.89[ASN][1000 genomes]
rs10844351	0.89[ASN][1000 genomes]
rs10844352	0.89[ASN][1000 genomes]
rs10844353	0.89[ASN][1000 genomes]
rs10844359	0.89[ASN][1000 genomes]
rs11052207	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052209	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052234	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052235	0.89[ASN][1000 genomes]
rs11052245	0.89[ASN][1000 genomes]
rs11052254	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052282	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1159189	0.89[ASN][1000 genomes]
rs11608817	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310789	0.89[ASN][1000 genomes]
rs12366653	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12366792	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12809846	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12830419	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831287	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1560008	0.89[ASN][1000 genomes]
rs16913477	0.89[ASN][1000 genomes]
rs1863871	0.89[ASN][1000 genomes]
rs2114869	0.89[ASN][1000 genomes]
rs2162657	0.89[ASN][1000 genomes]
rs2191964	0.89[ASN][1000 genomes]
rs34323946	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34833649	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34981673	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35015427	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35098654	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35181877	1.00[ASN][1000 genomes]
rs35280686	0.89[ASN][1000 genomes]
rs35561167	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35642909	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35671537	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35884213	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4140910	0.89[ASN][1000 genomes]
rs4763620	0.89[ASN][1000 genomes]
rs55873283	0.89[ASN][1000 genomes]
rs61916061	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488025	0.89[ASN][1000 genomes]
rs6488026	0.89[ASN][1000 genomes]
rs6488065	1.00[ASN][1000 genomes]
rs7132037	0.89[ASN][1000 genomes]
rs7136821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299738	0.89[ASN][1000 genomes]
rs7302110	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7302746	0.89[ASN][1000 genomes]
rs7303246	1.00[ASN][1000 genomes]
rs7304321	0.89[ASN][1000 genomes]
rs7304464	0.89[ASN][1000 genomes]
rs7305404	0.89[ASN][1000 genomes]
rs7305937	0.89[ASN][1000 genomes]
rs7306188	0.89[ASN][1000 genomes]
rs7309800	0.89[ASN][1000 genomes]
rs7310405	0.89[ASN][1000 genomes]
rs7310516	0.89[ASN][1000 genomes]
rs7310568	0.89[ASN][1000 genomes]
rs7310790	0.89[ASN][1000 genomes]
rs7311421	0.89[ASN][1000 genomes]
rs7311574	0.89[ASN][1000 genomes]
rs7311945	0.89[ASN][1000 genomes]
rs7313960	0.89[ASN][1000 genomes]
rs7959406	0.89[ASN][1000 genomes]
rs7959726	0.89[ASN][1000 genomes]
rs7961262	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7961416	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7962321	0.89[ASN][1000 genomes]
rs7967102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973603	0.89[ASN][1000 genomes]
rs7974871	0.89[ASN][1000 genomes]
rs7978187	0.89[ASN][1000 genomes]
rs958340	0.89[ASN][1000 genomes]
rs9919786	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12820641	CLEC2D	cis	Thyroid	GTEx
rs12820641	CLEC2D	cis	Esophagus Muscularis	GTEx
rs12820641	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9769400-9777400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr12:9770200-9786600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:9770400-9779400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:9771600-9794200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:9771600-9799200	Weak transcription	Fetal Lung	lung
6	chr12:9772400-9777600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:9773000-9779400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:9773400-9777200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:9775200-9777600	Weak transcription	Aorta	Aorta
10	chr12:9775800-9778000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:9776800-9777200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
12	chr12:9776800-9777800	ZNF genes & repeats	Primary T cells from cord blood	blood

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