Variant report

Variant	rs12819759
Chromosome Location	chr12:48115086-48115087
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10875683	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168187	0.86[ASN][1000 genomes]
rs11168194	0.81[JPT][hapmap]
rs11168212	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168219	0.86[ASN][1000 genomes]
rs11168220	0.82[ASN][1000 genomes]
rs11830795	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11834770	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1235152	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812460	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12812960	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12820269	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12828238	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2003471	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2074531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238144	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs2239188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283345	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285830	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3764015	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764016	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3764018	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764019	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4505143	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4537844	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133585	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs726588	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7302276	0.94[ASN][1000 genomes]
rs7306556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757284	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7967336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976708	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
6	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48102800-48125000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:48111400-48116000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:48111400-48124000	Weak transcription	Gastric	stomach
4	chr12:48111600-48115800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:48111800-48115200	Weak transcription	Primary T cells from cord blood	blood
6	chr12:48111800-48116000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:48111800-48117000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:48112000-48115200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:48112000-48115200	Weak transcription	HSMM	muscle
10	chr12:48112000-48115200	Weak transcription	HSMMtube	muscle
11	chr12:48112000-48115400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:48112000-48115400	Weak transcription	Osteobl	bone
13	chr12:48112000-48116000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:48112000-48116400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:48112000-48116400	Weak transcription	Psoas Muscle	Psoas
16	chr12:48112000-48117000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:48112000-48118200	Weak transcription	Fetal Intestine Large	intestine
18	chr12:48112000-48118400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:48112000-48120000	Weak transcription	Fetal Lung	lung
20	chr12:48112000-48120000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:48112000-48122800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:48112000-48123000	Weak transcription	Pancreas	Pancrea
23	chr12:48112000-48126800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:48112200-48115200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:48112200-48115200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:48112200-48115200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:48112200-48116400	Weak transcription	Aorta	Aorta
28	chr12:48112200-48116400	Weak transcription	Brain Angular Gyrus	brain
29	chr12:48112200-48116400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:48112200-48117200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:48112200-48118600	Weak transcription	Stomach Mucosa	stomach
32	chr12:48112200-48119000	Weak transcription	Colonic Mucosa	Colon
33	chr12:48112200-48119200	Weak transcription	GM12878-XiMat	blood
34	chr12:48112200-48125400	Weak transcription	Fetal Thymus	thymus
35	chr12:48112200-48127000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:48112400-48115400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:48112400-48115800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:48112400-48116400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:48112600-48115200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:48112600-48116200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:48112600-48116600	Weak transcription	Left Ventricle	heart
42	chr12:48112600-48116800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:48112600-48119000	Weak transcription	Right Atrium	heart
44	chr12:48112600-48119200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:48112600-48119400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:48112600-48122200	Weak transcription	Spleen	Spleen
47	chr12:48112600-48128600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:48112800-48115200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:48112800-48115400	Weak transcription	Brain Substantia Nigra	brain
50	chr12:48112800-48115600	Weak transcription	Brain Hippocampus Middle	brain

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