Variant report

Variant	rs3008625
Chromosome Location	chr1:222820022-222820023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222790877..222794262-chr1:222817668..222820285,3	MCF-7	breast:
2	chr1:222819105..222820831-chr1:222824168..222826539,3	K562	blood:
3	chr1:222815622..222820703-chr1:222883498..222888165,14	K562	blood:
4	chr1:222816842..222820047-chr1:222820781..222823646,5	K562	blood:
5	chr1:222817285..222820043-chr1:222820783..222823555,3	K562	blood:

Variant related genes	Relation type
ENSG00000162819	Chromatin interaction
ENSG00000186063	Chromatin interaction
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11485123	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12063226	0.82[EUR][1000 genomes]
rs1391557	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1391558	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498382	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17011666	0.83[AMR][1000 genomes]
rs17011686	0.92[ASN][1000 genomes]
rs17163450	0.83[ASN][1000 genomes]
rs17163468	0.83[ASN][1000 genomes]
rs1909195	0.83[AMR][1000 genomes]
rs1909197	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2030076	0.87[EUR][1000 genomes]
rs2088514	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133188	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2270707	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2378604	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2936020	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936023	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936049	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2936051	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2936052	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2936054	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3002129	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002146	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3002148	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008614	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3008615	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3008616	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008618	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008622	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3008629	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3008637	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34433664	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35507977	0.81[EUR][1000 genomes]
rs3811465	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61827168	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9441835	0.82[AMR][1000 genomes]
rs9441926	0.81[AMR][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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222818200-222823000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:222818200-222826000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:222818200-222826000	Weak transcription	Ovary	ovary
4	chr1:222818200-222826000	Weak transcription	Spleen	Spleen
5	chr1:222818200-222826200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:222818200-222826200	Weak transcription	Esophagus	oesophagus
7	chr1:222818400-222821000	Weak transcription	Fetal Kidney	kidney
8	chr1:222818400-222822200	Weak transcription	Lung	lung
9	chr1:222818400-222822400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:222818400-222822600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:222818400-222822800	Weak transcription	Colonic Mucosa	Colon
12	chr1:222818400-222823000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:222818400-222823000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:222818400-222823000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:222818400-222823200	Weak transcription	Brain Germinal Matrix	brain
16	chr1:222818400-222824000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:222818400-222824800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:222818400-222825600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:222818400-222825600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:222818400-222825600	Weak transcription	Psoas Muscle	Psoas
21	chr1:222818400-222825600	Weak transcription	Small Intestine	intestine
22	chr1:222818400-222826000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:222818400-222826000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:222818400-222826000	Weak transcription	Gastric	stomach
25	chr1:222818400-222826000	Weak transcription	Pancreas	Pancrea
26	chr1:222818400-222826000	Weak transcription	Right Ventricle	heart
27	chr1:222818400-222826200	Weak transcription	Aorta	Aorta
28	chr1:222818400-222826600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:222818400-222827600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:222818400-222833600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:222818600-222820200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:222818600-222820400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:222818600-222820800	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr1:222818600-222820800	Weak transcription	Fetal Thymus	thymus
35	chr1:222818600-222821200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:222818800-222820200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:222818800-222821400	Weak transcription	Fetal Brain Female	brain
38	chr1:222818800-222822200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:222818800-222822600	Weak transcription	HUVEC	blood vessel
40	chr1:222818800-222822800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:222818800-222823000	Weak transcription	Fetal Brain Male	brain
42	chr1:222818800-222823000	Weak transcription	HSMMtube	muscle
43	chr1:222818800-222823200	Weak transcription	Brain Angular Gyrus	brain
44	chr1:222818800-222823200	Weak transcription	Brain Anterior Caudate	brain
45	chr1:222818800-222823200	Weak transcription	Brain Substantia Nigra	brain
46	chr1:222818800-222823800	Weak transcription	HMEC	breast
47	chr1:222818800-222826000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:222818800-222826000	Weak transcription	Fetal Heart	heart
49	chr1:222818800-222841600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:222819000-222820200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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