Variant report

Variant	rs2818888
Chromosome Location	chr1:247088863-247088864
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	chr1:247070542..247073488-chr1:247087102..247088901,2	K562	blood:
2	chr1:247071846..247074365-chr1:247086927..247089836,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1039009	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1039010	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11585741	0.88[EUR][1000 genomes]
rs1472275	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1612610	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1613209	0.91[EUR][1000 genomes]
rs1619941	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1691240	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1691241	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1691242	0.88[AMR][1000 genomes]
rs1691252	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1691254	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1691255	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1779964	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1779968	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1779969	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2172796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2642975	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2642977	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2642990	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2642991	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2800214	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2800215	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2800219	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2800220	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2800221	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7542895	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs768197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9729306	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9729316	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv873425	chr1:247069514-247156066	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv873426	chr1:247069514-247162628	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247055400-247089000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:247061200-247093000	Weak transcription	Fetal Brain Male	brain
3	chr1:247069600-247093400	Weak transcription	Colonic Mucosa	Colon
4	chr1:247069600-247093400	Weak transcription	Esophagus	oesophagus
5	chr1:247069800-247093800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:247070000-247093600	Weak transcription	Aorta	Aorta
7	chr1:247070800-247092800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:247071000-247093400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:247073600-247089200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:247074200-247093400	Weak transcription	NHLF	lung
11	chr1:247078400-247093600	Weak transcription	Fetal Kidney	kidney
12	chr1:247078600-247089000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:247078600-247093400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:247078800-247093400	Weak transcription	Fetal Intestine Large	intestine
15	chr1:247079200-247089000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:247080400-247093400	Weak transcription	Stomach Mucosa	stomach
17	chr1:247080800-247089800	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:247080800-247092000	Weak transcription	NHEK	skin
19	chr1:247081000-247089000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:247081000-247089000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:247081000-247089000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:247081000-247089400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:247081000-247092400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:247081000-247093400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:247081000-247093400	Weak transcription	HSMMtube	muscle
26	chr1:247081200-247089000	Weak transcription	Thymus	Thymus
27	chr1:247081200-247089000	Weak transcription	HMEC	breast
28	chr1:247081200-247093400	Weak transcription	NH-A	brain
29	chr1:247082000-247089000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:247082000-247089000	Weak transcription	Fetal Thymus	thymus
31	chr1:247082000-247089400	Weak transcription	Primary B cells from cord blood	blood
32	chr1:247082400-247092000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:247082800-247089400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:247083200-247089400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:247084400-247089400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:247085000-247089800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:247085200-247089800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:247085400-247092200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:247085400-247093400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:247085600-247093400	Weak transcription	Osteobl	bone
41	chr1:247085800-247089400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:247085800-247093000	Weak transcription	Placenta	Placenta
43	chr1:247085800-247093400	Weak transcription	HUVEC	blood vessel
44	chr1:247086800-247089000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr1:247086800-247089400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:247086800-247089600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:247086800-247089800	Genic enhancers	K562	blood
48	chr1:247086800-247092600	ZNF genes & repeats	GM12878-XiMat	blood
49	chr1:247086800-247093400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:247087000-247092800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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