Variant report

Variant	rs6488507
Chromosome Location	chr12:12356900-12356901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10743980	0.86[JPT][hapmap]
rs10772536	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10772537	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10772540	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10845489	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10845491	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10845492	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10845494	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845495	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845501	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11054718	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11054721	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11054724	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054731	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11054744	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11054754	0.81[CEU][hapmap]
rs11609634	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12366664	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12823243	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17819999	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1819871	0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2284396	0.93[CEU][hapmap];0.82[AMR][1000 genomes]
rs2302684	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2417085	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2417086	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782528	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4477532	0.93[CEU][hapmap];0.82[AMR][1000 genomes]
rs4763785	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61920859	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7294695	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7302808	0.80[EUR][1000 genomes]
rs7305037	0.96[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7956548	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7956971	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7966410	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7979447	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
2	chr12:12315400-12371600	Weak transcription	Lung	lung
3	chr12:12325400-12360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:12334400-12367600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:12335200-12365800	Weak transcription	NHEK	skin
6	chr12:12336200-12360000	Weak transcription	Aorta	Aorta
7	chr12:12336200-12363200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:12336200-12369800	Weak transcription	Left Ventricle	heart
9	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
10	chr12:12336400-12357400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:12339200-12357600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:12340600-12359400	Weak transcription	Ovary	ovary
13	chr12:12342200-12360000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:12344000-12367800	Weak transcription	NHLF	lung
15	chr12:12344200-12367200	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:12344200-12367400	Weak transcription	Brain Substantia Nigra	brain
17	chr12:12344200-12367800	Weak transcription	NH-A	brain
18	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
19	chr12:12347600-12367800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:12348800-12367000	Weak transcription	HUVEC	blood vessel
21	chr12:12349000-12367600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:12351400-12361800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:12351800-12360000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:12352200-12362000	Weak transcription	Brain Angular Gyrus	brain
25	chr12:12352200-12367200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:12352400-12360600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:12352600-12364400	Weak transcription	HSMM	muscle
28	chr12:12352600-12367600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:12353200-12358200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:12353200-12367400	Weak transcription	Fetal Kidney	kidney
31	chr12:12353400-12357400	Weak transcription	Fetal Brain Female	brain
32	chr12:12353400-12367000	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:12353800-12359800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:12354600-12367800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:12354800-12370400	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:12355000-12367800	Weak transcription	Gastric	stomach
37	chr12:12355400-12367400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:12355400-12367600	Weak transcription	Osteobl	bone
39	chr12:12355400-12369400	Weak transcription	Adipose Nuclei	Adipose
40	chr12:12355600-12357200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr12:12355600-12357400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr12:12355600-12365800	Weak transcription	Fetal Intestine Small	intestine
43	chr12:12355600-12367600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:12355600-12367600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:12355600-12367800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:12355600-12367800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:12355600-12367800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:12355600-12369800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:12355800-12357200	Enhancers	Stomach Mucosa	stomach
50	chr12:12355800-12357400	Weak transcription	Fetal Stomach	stomach

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