Variant report

Variant	rs11054738
Chromosome Location	chr12:12388027-12388028
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10845493	0.84[CEU][hapmap]
rs11054736	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054741	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1181332	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1181334	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12372237	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817910	1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12820350	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12823867	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34201398	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35172905	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4763790	0.81[AMR][1000 genomes]
rs56084505	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61920856	0.92[ASN][1000 genomes]
rs71457140	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:12370800-12392200	Weak transcription	Brain Substantia Nigra	brain
3	chr12:12377800-12407200	Weak transcription	NH-A	brain
4	chr12:12379200-12396800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:12379400-12393600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:12379600-12393600	Weak transcription	NHLF	lung
7	chr12:12380200-12388800	Weak transcription	Fetal Intestine Small	intestine
8	chr12:12380800-12388400	Weak transcription	Fetal Stomach	stomach
9	chr12:12381400-12393600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:12381600-12390000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:12381800-12391800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:12381800-12393000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:12382000-12389400	Weak transcription	Psoas Muscle	Psoas
14	chr12:12382000-12392000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:12382000-12393800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:12383000-12393600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:12383000-12393800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:12383000-12394200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:12383200-12389800	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:12384800-12389200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:12384800-12389400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:12384800-12389400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:12384800-12389600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:12384800-12389800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:12384800-12390000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:12384800-12392000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:12384800-12417200	Weak transcription	K562	blood
28	chr12:12385000-12388600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:12385000-12389200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:12385000-12389400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:12385000-12389400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:12385000-12390000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:12385000-12390000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:12385000-12392000	Weak transcription	Brain Angular Gyrus	brain
35	chr12:12385000-12393600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:12385000-12393600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:12385000-12393600	Weak transcription	Ovary	ovary
38	chr12:12385000-12394600	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:12385000-12396600	Weak transcription	Left Ventricle	heart
40	chr12:12385000-12396800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:12385000-12404000	Weak transcription	Lung	lung
42	chr12:12385000-12417800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr12:12385200-12409200	Weak transcription	Pancreas	Pancrea
44	chr12:12386000-12390000	Weak transcription	Brain Anterior Caudate	brain
45	chr12:12386600-12396800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:12387000-12389800	Weak transcription	HepG2	liver
47	chr12:12387400-12389800	Weak transcription	Liver	Liver
48	chr12:12388000-12388200	Enhancers	A549	lung
49	chr12:12388000-12389000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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