Variant report

Variant	rs12830419
Chromosome Location	chr12:9762813-9762814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1008611	1.00[JPT][hapmap]
rs10466762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10743776	0.89[ASN][1000 genomes]
rs10743820	1.00[JPT][hapmap]
rs10743822	1.00[JPT][hapmap]
rs10772005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10772006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10772104	1.00[JPT][hapmap]
rs10772119	1.00[JPT][hapmap]
rs10772120	1.00[JPT][hapmap]
rs10844236	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844267	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844327	0.89[ASN][1000 genomes]
rs10844350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10844351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10844352	0.89[ASN][1000 genomes]
rs10844353	0.89[ASN][1000 genomes]
rs10844359	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10844372	1.00[JPT][hapmap]
rs10844418	1.00[JPT][hapmap]
rs10844424	1.00[JPT][hapmap]
rs10844429	1.00[JPT][hapmap]
rs10844780	1.00[JPT][hapmap]
rs11052207	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052209	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052235	0.89[ASN][1000 genomes]
rs11052241	1.00[JPT][hapmap]
rs11052245	0.89[ASN][1000 genomes]
rs11052254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052282	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11052430	1.00[JPT][hapmap]
rs11053051	1.00[JPT][hapmap]
rs1159189	0.89[ASN][1000 genomes]
rs11608817	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310789	0.89[ASN][1000 genomes]
rs12366653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12366792	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12368445	1.00[JPT][hapmap]
rs12578928	1.00[JPT][hapmap]
rs12809846	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12810851	1.00[JPT][hapmap]
rs12820641	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823699	1.00[JPT][hapmap]
rs12824491	1.00[JPT][hapmap]
rs12825507	1.00[JPT][hapmap]
rs12828602	1.00[JPT][hapmap]
rs12831287	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12831453	1.00[JPT][hapmap]
rs1560008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16913477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1863871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1990533	1.00[JPT][hapmap]
rs2114869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2114872	1.00[JPT][hapmap]
rs2162657	0.89[ASN][1000 genomes]
rs2191964	0.89[ASN][1000 genomes]
rs2401396	1.00[JPT][hapmap]
rs2401397	1.00[JPT][hapmap]
rs2401398	1.00[JPT][hapmap]
rs3176800	1.00[JPT][hapmap]
rs3176802	1.00[JPT][hapmap]
rs3176806	1.00[JPT][hapmap]
rs34323946	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34833649	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34981673	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35015427	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35098654	0.87[AFR][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	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35642909	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35671537	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35884213	0.82[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	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6416258	1.00[JPT][hapmap]
rs6488025	0.89[ASN][1000 genomes]
rs6488026	0.89[ASN][1000 genomes]
rs6488065	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs704223	1.00[JPT][hapmap]
rs7132037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7136821	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299738	0.89[ASN][1000 genomes]
rs7302110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7302746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7303246	1.00[ASN][1000 genomes]
rs7304321	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7304464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7305404	0.89[ASN][1000 genomes]
rs7305937	0.89[ASN][1000 genomes]
rs7306188	0.89[ASN][1000 genomes]
rs7309800	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7310405	0.89[ASN][1000 genomes]
rs7310516	0.89[ASN][1000 genomes]
rs7310568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7310790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7310897	1.00[JPT][hapmap]
rs7311421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7311574	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7311945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7312624	1.00[JPT][hapmap]
rs7313960	0.89[ASN][1000 genomes]
rs7315769	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7959406	0.89[ASN][1000 genomes]
rs7959726	0.89[ASN][1000 genomes]
rs7961262	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7961416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7962321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7967102	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973603	0.89[ASN][1000 genomes]
rs7974871	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7978187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs929615	1.00[JPT][hapmap]
rs958340	0.89[ASN][1000 genomes]
rs9630265	1.00[JPT][hapmap]
rs982511	1.00[JPT][hapmap]
rs9919786	1.00[CHB][hapmap];1.00[JPT][hapmap];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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12830419	CLEC2D	cis	Esophagus Muscularis	GTEx
rs12830419	LOC374443	Cis_1M	lymphoblastoid	RTeQTL
rs12830419	LOC728715///OVOS2	Cis_chr	lymphoblastoid	RTeQTL
rs12830419	CLEC2D	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9734400-9763000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:9755800-9771200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:9757200-9763000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:9759200-9771200	Weak transcription	Fetal Lung	lung
5	chr12:9760800-9763000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:9760800-9763000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:9760800-9763000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:9760800-9767600	Weak transcription	Thymus	Thymus
9	chr12:9760800-9767800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:9761000-9763200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:9761000-9767200	Weak transcription	Primary T cells from cord blood	blood
12	chr12:9761200-9763000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:9762400-9764200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr12:9762800-9763600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:9762800-9763600	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:9762800-9763800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:9762800-9764000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr12:9762800-9764000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr12:9762800-9764000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:9762800-9764200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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