Variant report

Variant	rs12370579
Chromosome Location	chr12:9856826-9856827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1008611	0.83[ASN][1000 genomes]
rs10743821	0.83[ASN][1000 genomes]
rs10743822	0.83[ASN][1000 genomes]
rs10772060	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10844418	1.00[CHB][hapmap]
rs10844424	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs10844429	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs11052430	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.84[MKK][hapmap]
rs11052431	1.00[CHB][hapmap];0.84[MKK][hapmap]
rs11052552	0.90[LWK][hapmap]
rs11052718	0.83[ASN][1000 genomes]
rs11052785	0.83[ASN][1000 genomes]
rs12369995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371981	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578698	0.83[ASN][1000 genomes]
rs12578928	1.00[CHB][hapmap]
rs12582616	0.83[ASN][1000 genomes]
rs12809752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810851	1.00[CHB][hapmap]
rs12812783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823653	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823699	1.00[CHB][hapmap]
rs12825507	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs12828602	1.00[CHB][hapmap]
rs12830448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861089	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1990533	0.83[ASN][1000 genomes]
rs2080207	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2114872	1.00[CHB][hapmap]
rs2192433	0.83[ASN][1000 genomes]
rs2192434	0.83[ASN][1000 genomes]
rs2192435	0.83[ASN][1000 genomes]
rs2192439	0.89[ASN][1000 genomes]
rs2401396	0.83[ASN][1000 genomes]
rs34201389	0.83[ASN][1000 genomes]
rs34623781	0.89[ASN][1000 genomes]
rs34826829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35078787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35512621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763280	1.00[ASN][1000 genomes]
rs4763813	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs4763814	1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4763819	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4763835	0.83[ASN][1000 genomes]
rs61913428	0.83[ASN][1000 genomes]
rs66725265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67429242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71441764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310897	1.00[CHB][hapmap]
rs7485402	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7954062	0.89[ASN][1000 genomes]
rs7961812	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961903	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7974554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975557	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975865	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630265	1.00[CHB][hapmap]
rs982511	1.00[CHD][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2757490	chr12:9855958-9888553	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12370579	DCAL1	cis	multi-tissue	Pritchard
rs12370579	CLEC2D	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:9841800-9863200	Weak transcription	HSMMtube	muscle
3	chr12:9844200-9860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:9847600-9860000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:9848200-9860200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:9848400-9860200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:9848600-9859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:9849800-9860600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:9853400-9858400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr12:9853400-9858400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:9854600-9860000	Weak transcription	Left Ventricle	heart
12	chr12:9854800-9860000	Weak transcription	Spleen	Spleen
13	chr12:9855000-9857000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:9855000-9857400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:9855000-9860200	Enhancers	Primary T cells from cord blood	blood
16	chr12:9855200-9858800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:9855200-9860000	Weak transcription	Esophagus	oesophagus
18	chr12:9855400-9858600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:9855600-9858200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:9855600-9860200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr12:9855600-9860600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:9855600-9862800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:9855800-9858600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:9855800-9858600	Weak transcription	Thymus	Thymus
25	chr12:9856200-9858000	Weak transcription	Primary B cells from cord blood	blood
26	chr12:9856200-9860000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:9856200-9860000	Weak transcription	Fetal Thymus	thymus
28	chr12:9856400-9857600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:9856400-9858600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr12:9856400-9858600	Weak transcription	Dnd41	blood
31	chr12:9856600-9857200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:9856600-9857800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr12:9856600-9858000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:9856800-9858000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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