Variant report

Variant	rs2994960
Chromosome Location	chr1:241588127-241588128
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10926485	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409402	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1341469	0.84[AFR][1000 genomes]
rs2185625	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2994963	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2994965	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2994966	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3014551	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3014552	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3014553	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3014554	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3014556	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014557	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121204	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660084	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5012572	0.81[ASN][1000 genomes]
rs55825634	0.89[ASN][1000 genomes]
rs6679243	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6696080	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9428875	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9428876	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv549461	chr1:241554603-241639401	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv873369	chr1:241566725-241596093	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv873370	chr1:241566725-241608619	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241586600-241588200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:241586600-241588200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:241586600-241588200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:241586600-241588200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:241586800-241588200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:241586800-241588200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:241586800-241588200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:241586800-241588200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:241586800-241588200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:241586800-241588200	Active TSS	Fetal Brain Female	brain
11	chr1:241586800-241588200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:241587000-241588200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:241587000-241588200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:241587000-241588200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr1:241587000-241588200	Active TSS	Muscle Satellite Cultured Cells	--
16	chr1:241587000-241588200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
17	chr1:241587000-241588200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
18	chr1:241587200-241588200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:241587200-241588200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr1:241587200-241588200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr1:241587200-241588200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:241587200-241588200	Active TSS	Brain Angular Gyrus	brain
23	chr1:241587200-241588200	Active TSS	Brain Anterior Caudate	brain
24	chr1:241587200-241588200	Enhancers	Fetal Brain Male	brain
25	chr1:241587600-241588200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:241587600-241588200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
27	chr1:241587600-241588200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
28	chr1:241587600-241588200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:241587600-241588200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:241587600-241588200	Bivalent/Poised TSS	Colonic Mucosa	Colon
31	chr1:241587600-241588200	Flanking Active TSS	HUVEC	blood vessel
32	chr1:241587600-241588200	Flanking Active TSS	NHDF-Ad	bronchial
33	chr1:241587800-241588200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr1:241587800-241588200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:241587800-241588200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:241587800-241588200	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr1:241587800-241588200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr1:241587800-241588200	Bivalent Enhancer	Psoas Muscle	Psoas
39	chr1:241587800-241588200	Flanking Active TSS	Osteobl	bone
40	chr1:241588000-241588200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:241588000-241588200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
42	chr1:241588000-241588200	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:241588000-241588200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
44	chr1:241588000-241588200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr1:241588000-241588200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:241588000-241588200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
47	chr1:241588000-241588200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:241588000-241588200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:241588000-241588200	Bivalent Enhancer	Fetal Stomach	stomach
50	chr1:241588000-241588200	Bivalent Enhancer	Stomach Smooth Muscle	stomach

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