Variant report

Variant	rs2690123
Chromosome Location	chr6:25306363-25306364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12055533	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196702	0.82[ASN][1000 genomes]
rs1989206	0.97[ASN][1000 genomes]
rs2143022	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2252012	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328878	0.96[ASN][1000 genomes]
rs2690109	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2690115	0.85[ASN][1000 genomes]
rs2690120	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690125	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690127	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2690129	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690131	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744290	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2744296	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744299	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2744302	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2744303	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4712908	0.83[ASN][1000 genomes]
rs9348670	0.96[ASN][1000 genomes]
rs9356973	0.96[ASN][1000 genomes]
rs9358850	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9358851	0.96[ASN][1000 genomes]
rs9379751	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467465	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:25294200-25311200	Weak transcription	Lung	lung
3	chr6:25298000-25311800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:25301400-25313400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:25301600-25311600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:25302000-25312800	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:25302600-25311200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:25302600-25312400	Weak transcription	Thymus	Thymus
9	chr6:25302800-25307600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:25302800-25312200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:25303200-25306400	Weak transcription	Brain Anterior Caudate	brain
12	chr6:25303200-25308200	Weak transcription	Ovary	ovary
13	chr6:25303200-25311200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:25303200-25311600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:25303200-25314800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:25303400-25306400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr6:25303400-25306600	Weak transcription	Aorta	Aorta
18	chr6:25303400-25306800	Enhancers	Duodenum Mucosa	Duodenum
19	chr6:25303400-25310200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:25303400-25311600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:25303400-25315400	Weak transcription	Fetal Kidney	kidney
22	chr6:25303800-25308000	Weak transcription	Fetal Heart	heart
23	chr6:25303800-25308000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:25303800-25308000	Weak transcription	HSMMtube	muscle
25	chr6:25303800-25311800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:25303800-25312400	Weak transcription	Adipose Nuclei	Adipose
27	chr6:25304000-25307400	Weak transcription	Stomach Mucosa	stomach
28	chr6:25304000-25308200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:25304000-25311400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:25304000-25311600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:25304200-25309400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:25304200-25310200	Weak transcription	NHLF	lung
33	chr6:25304200-25311400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:25305000-25310400	Weak transcription	Right Atrium	heart
35	chr6:25305000-25311200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
37	chr6:25305400-25311600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr6:25305600-25308000	Weak transcription	Fetal Intestine Large	intestine
39	chr6:25305600-25311600	Weak transcription	Fetal Lung	lung
40	chr6:25305600-25311800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:25305800-25306800	Weak transcription	Small Intestine	intestine
42	chr6:25306000-25306600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:25306000-25307400	Weak transcription	Fetal Intestine Small	intestine
44	chr6:25306000-25310200	Weak transcription	A549	lung
45	chr6:25306200-25306800	Enhancers	Sigmoid Colon	Sigmoid Colon

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