Variant report

Variant	rs11054724
Chromosome Location	chr12:12345893-12345894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10492120	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10743980	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10772536	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10772537	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10772540	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10772542	0.90[CHB][hapmap]
rs10772547	0.90[CHB][hapmap]
rs10845489	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs10845491	0.87[AMR][1000 genomes]
rs10845492	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10845494	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845495	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845501	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11054718	0.85[AMR][1000 genomes]
rs11054721	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11054731	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11054744	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11054754	0.81[CHB][hapmap]
rs11609634	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs12366664	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12823243	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17819999	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1819871	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2284396	0.89[CEU][hapmap]
rs2302684	0.82[AMR][1000 genomes]
rs2417085	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2417086	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782528	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4477532	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs4763785	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61920859	0.86[EUR][1000 genomes]
rs6488507	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]
rs7294695	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs7305037	0.93[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7956548	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7956971	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7966410	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7973531	0.90[CHB][hapmap]
rs7979447	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:12312000-12350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
5	chr12:12315400-12371600	Weak transcription	Lung	lung
6	chr12:12325400-12360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:12334200-12350800	Weak transcription	Fetal Thymus	thymus
8	chr12:12334400-12348400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:12334400-12349200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:12334400-12349600	Weak transcription	Dnd41	blood
11	chr12:12334400-12351200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:12334400-12352000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:12334400-12354000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:12334400-12367600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:12334600-12349200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:12334800-12346800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:12334800-12352800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:12335200-12352000	Weak transcription	HSMM	muscle
19	chr12:12335200-12365800	Weak transcription	NHEK	skin
20	chr12:12335800-12354000	Weak transcription	HSMMtube	muscle
21	chr12:12336000-12352000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:12336000-12354200	Weak transcription	Primary T cells from cord blood	blood
23	chr12:12336000-12355600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:12336200-12347000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:12336200-12360000	Weak transcription	Aorta	Aorta
26	chr12:12336200-12363200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:12336200-12369800	Weak transcription	Left Ventricle	heart
28	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
29	chr12:12336400-12348800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:12336400-12349600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:12336400-12357400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:12337600-12348200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:12337800-12348400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:12338200-12349000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:12338200-12355800	Weak transcription	Stomach Mucosa	stomach
36	chr12:12339000-12350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:12339200-12357600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:12339800-12350600	Weak transcription	Fetal Intestine Small	intestine
39	chr12:12339800-12350600	Weak transcription	Fetal Stomach	stomach
40	chr12:12340000-12346600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:12340000-12348600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:12340200-12349600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:12340600-12349600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:12340600-12359400	Weak transcription	Ovary	ovary
45	chr12:12340800-12349600	Weak transcription	Liver	Liver
46	chr12:12341000-12346400	Weak transcription	HepG2	liver
47	chr12:12341800-12347000	Weak transcription	Fetal Lung	lung
48	chr12:12342200-12360000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr12:12343800-12347000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:12344000-12349000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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