Variant report

Variant	rs2666487
Chromosome Location	chr1:62751985-62751986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62750576..62752122-chr1:62863647..62866549,2	K562	blood:
2	chr1:62750494..62753386-chr1:62754498..62756263,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10493320	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11207957	0.86[ASN][1000 genomes]
rs12058486	0.94[ASN][1000 genomes]
rs12063531	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12065844	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12078087	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12079207	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12082238	0.98[ASN][1000 genomes]
rs12085325	0.98[ASN][1000 genomes]
rs12718429	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12724349	0.94[ASN][1000 genomes]
rs12760226	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12760895	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2296518	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2477872	1.00[ASN][1000 genomes]
rs2666488	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666503	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666506	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666507	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666508	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2765251	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2765258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765261	0.98[ASN][1000 genomes]
rs2765263	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34752481	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516290	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7520614	1.00[ASN][1000 genomes]
rs765691	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs765692	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs912894	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs912895	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs912896	0.89[AMR][1000 genomes];0.94[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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62748400-62752400	Enhancers	Fetal Muscle Leg	muscle
2	chr1:62749000-62753000	Enhancers	Fetal Lung	lung
3	chr1:62750000-62752000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr1:62750200-62752000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:62750800-62752200	Enhancers	Gastric	stomach
6	chr1:62750800-62753200	Enhancers	HMEC	breast
7	chr1:62751000-62752600	Bivalent Enhancer	Fetal Intestine Large	intestine
8	chr1:62751000-62753000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:62751200-62752200	Bivalent Enhancer	NH-A	brain
10	chr1:62751200-62753400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:62751400-62752600	Enhancers	A549	lung
12	chr1:62751400-62752800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:62751400-62753200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
14	chr1:62751600-62752000	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr1:62751600-62752000	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr1:62751600-62752000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:62751600-62752000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr1:62751600-62752000	Flanking Active TSS	Pancreas	Pancrea
19	chr1:62751600-62752000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr1:62751600-62752200	Flanking Active TSS	Colonic Mucosa	Colon
21	chr1:62751600-62752200	Active TSS	Rectal Smooth Muscle	rectum
22	chr1:62751600-62752200	Enhancers	Right Atrium	heart
23	chr1:62751600-62752400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
24	chr1:62751600-62752400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
25	chr1:62751600-62752400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:62751600-62752400	Enhancers	Adipose Nuclei	Adipose
27	chr1:62751600-62752400	Bivalent Enhancer	Brain Germinal Matrix	brain
28	chr1:62751600-62752600	Enhancers	Liver	Liver
29	chr1:62751600-62752600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
30	chr1:62751600-62752800	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
31	chr1:62751600-62752800	Bivalent Enhancer	Fetal Brain Male	brain
32	chr1:62751600-62753000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
33	chr1:62751600-62753000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
34	chr1:62751600-62753000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
35	chr1:62751600-62753000	Bivalent Enhancer	Fetal Stomach	stomach
36	chr1:62751600-62753200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:62751600-62753200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:62751600-62753200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
39	chr1:62751600-62753200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr1:62751600-62753400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
41	chr1:62751600-62754200	Enhancers	Placenta	Placenta
42	chr1:62751600-62754800	Enhancers	Fetal Heart	heart
43	chr1:62751600-62755000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:62751600-62756200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:62751800-62752000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:62751800-62752000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:62751800-62752000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr1:62751800-62752000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
49	chr1:62751800-62752000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
50	chr1:62751800-62752000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum

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