Variant report

Variant	rs55754162
Chromosome Location	chr12:86229120-86229121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs17345327	0.83[EUR][1000 genomes]
rs1800832	0.86[EUR][1000 genomes]
rs55644633	0.81[EUR][1000 genomes]
rs55694421	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55736533	0.90[EUR][1000 genomes]
rs55746689	0.81[EUR][1000 genomes]
rs55758854	0.85[EUR][1000 genomes]
rs55795518	0.85[EUR][1000 genomes]
rs55811116	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55811700	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55853578	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55856700	0.90[EUR][1000 genomes]
rs55899243	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55900789	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55926212	0.90[EUR][1000 genomes]
rs55966514	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56020312	0.85[EUR][1000 genomes]
rs56055322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56169451	0.83[EUR][1000 genomes]
rs56208754	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56298026	0.83[EUR][1000 genomes]
rs56323012	0.81[EUR][1000 genomes]
rs61928894	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61928895	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61928896	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61928898	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61928900	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61928903	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61928904	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61928908	0.90[EUR][1000 genomes]
rs61928913	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928917	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928918	0.84[EUR][1000 genomes]
rs61928956	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928957	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928958	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928959	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930060	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930062	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930069	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930070	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930071	0.89[AMR][1000 genomes]
rs61930072	0.84[AMR][1000 genomes]
rs61930073	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930079	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930080	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930082	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930122	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930124	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930128	0.90[EUR][1000 genomes]
rs61930130	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930131	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930135	0.90[EUR][1000 genomes]
rs61930136	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930584	0.82[EUR][1000 genomes]
rs61930595	0.85[EUR][1000 genomes]
rs61930642	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930643	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930649	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930651	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930652	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930653	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930863	0.90[EUR][1000 genomes]
rs61930876	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930878	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61930880	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61930881	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61930882	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61930895	0.83[EUR][1000 genomes]
rs7962310	0.90[EUR][1000 genomes]
rs7973110	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1052187	chr12:85954455-86278200	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv541560	chr12:85954455-86278200	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1049443	chr12:86185887-86272493	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
7	esv1797806	chr12:86198935-86425608	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1036914	chr12:86201703-86272493	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86219800-86229400	Weak transcription	Stomach Mucosa	stomach
2	chr12:86223200-86229600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:86224800-86230400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr12:86225200-86229400	Weak transcription	NHDF-Ad	bronchial
5	chr12:86226800-86230400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:86227200-86229200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:86227200-86230600	Active TSS	Right Atrium	heart
8	chr12:86227400-86230200	Active TSS	HMEC	breast
9	chr12:86227600-86230400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:86227600-86230600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:86227800-86229400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr12:86227800-86230400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:86227800-86230400	Active TSS	Aorta	Aorta
14	chr12:86227800-86230400	Active TSS	Fetal Stomach	stomach
15	chr12:86227800-86231000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr12:86228000-86230200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:86228000-86230400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr12:86228000-86230400	Active TSS	Hela-S3	cervix
19	chr12:86228000-86230600	Active TSS	Fetal Kidney	kidney
20	chr12:86228200-86229200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:86228200-86229200	Weak transcription	Fetal Lung	lung
22	chr12:86228200-86229800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:86228200-86230400	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr12:86228200-86230400	Active TSS	A549	lung
25	chr12:86228400-86229200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr12:86228400-86229200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:86228400-86229200	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:86228400-86229200	Weak transcription	Fetal Heart	heart
29	chr12:86228400-86229200	Weak transcription	Fetal Intestine Small	intestine
30	chr12:86228400-86229200	Weak transcription	Left Ventricle	heart
31	chr12:86228400-86229400	Weak transcription	Ovary	ovary
32	chr12:86228400-86230000	Active TSS	NH-A	brain
33	chr12:86228400-86230200	Active TSS	Adipose Nuclei	Adipose
34	chr12:86228400-86230200	Active TSS	NHEK	skin
35	chr12:86228400-86230400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:86228400-86230400	Active TSS	Osteobl	bone
37	chr12:86228600-86229200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:86228600-86229600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:86228600-86229800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:86228800-86229200	Active TSS	Fetal Intestine Large	intestine
41	chr12:86228800-86229200	Enhancers	HSMMtube	muscle
42	chr12:86228800-86229400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:86228800-86230400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:86228800-86230400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr12:86229000-86229400	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr12:86229000-86229400	Enhancers	HSMM	muscle
47	chr12:86229000-86229400	Active TSS	HUVEC	blood vessel
48	chr12:86229000-86229600	Active TSS	Liver	Liver
49	chr12:86229000-86230400	Active TSS	Duodenum Mucosa	Duodenum
50	chr12:86229000-86230400	Active TSS	Fetal Muscle Leg	muscle

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