Variant report

Variant	rs41312020
Chromosome Location	chr1:45469586-45469587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45466176..45467776-chr1:45467983..45470171,2	MCF-7	breast:
2	chr1:45284388..45285918-chr1:45466927..45469619,2	MCF-7	breast:
3	chr1:45187000..45190242-chr1:45468386..45470693,3	K562	blood:
4	chr1:45467917..45470543-chr1:45471349..45473088,2	MCF-7	breast:
5	chr1:45284681..45289780-chr1:45466475..45469909,5	MCF-7	breast:
6	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
7	chr1:45469387..45472063-chr1:45473604..45475987,2	MCF-7	breast:
8	chr1:45450854..45457330-chr1:45465047..45472849,14	K562	blood:
9	chr1:45469532..45472999-chr1:45473175..45475841,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000117425	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000232369	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11548990	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969084	0.87[AMR][1000 genomes]
rs1995403	0.87[AMR][1000 genomes]
rs2228084	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234480	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346704	0.87[AMR][1000 genomes]
rs4660835	0.87[AMR][1000 genomes]
rs59432881	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429556	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6664113	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6693885	0.89[ASN][1000 genomes]
rs72676543	0.88[EUR][1000 genomes]
rs72684406	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684412	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684416	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72684425	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72684426	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72684447	0.87[AMR][1000 genomes]
rs7528534	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7543211	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45452800-45475200	Weak transcription	Right Atrium	heart
2	chr1:45465000-45470200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:45466000-45469600	Weak transcription	Hela-S3	cervix
4	chr1:45466600-45469600	Weak transcription	HUVEC	blood vessel
5	chr1:45466600-45470000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:45466600-45474800	Strong transcription	Fetal Brain Female	brain
7	chr1:45466600-45475000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:45466800-45469600	Weak transcription	HSMMtube	muscle
9	chr1:45466800-45470000	Weak transcription	HMEC	breast
10	chr1:45466800-45470200	Weak transcription	NHDF-Ad	bronchial
11	chr1:45466800-45475000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr1:45466800-45475200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:45466800-45475200	Strong transcription	Primary T cells from cord blood	blood
14	chr1:45466800-45475200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:45466800-45475200	Strong transcription	Fetal Stomach	stomach
16	chr1:45467000-45470400	Weak transcription	Fetal Kidney	kidney
17	chr1:45467000-45473200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:45467000-45474400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr1:45467000-45474800	Strong transcription	Colonic Mucosa	Colon
20	chr1:45467000-45475200	Strong transcription	NHLF	lung
21	chr1:45467000-45475400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:45467000-45475400	Weak transcription	Psoas Muscle	Psoas
23	chr1:45467000-45476400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:45467200-45470000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:45467200-45470000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:45467200-45474400	Strong transcription	Brain Germinal Matrix	brain
27	chr1:45467200-45475200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:45467400-45474800	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:45467400-45474800	Strong transcription	Spleen	Spleen
30	chr1:45467400-45475000	Strong transcription	Esophagus	oesophagus
31	chr1:45467400-45475200	Strong transcription	Lung	lung
32	chr1:45467400-45475200	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr1:45467400-45475400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:45467400-45475400	Strong transcription	Fetal Thymus	thymus
35	chr1:45467400-45475400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:45467600-45472400	Strong transcription	NHEK	skin
37	chr1:45467600-45473800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:45467600-45474000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr1:45467600-45474600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:45467600-45474600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:45467600-45474800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:45467600-45474800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:45467600-45474800	Strong transcription	Brain Angular Gyrus	brain
44	chr1:45467600-45474800	Strong transcription	Placenta	Placenta
45	chr1:45467600-45474800	Strong transcription	Ovary	ovary
46	chr1:45467600-45475000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:45467600-45475000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:45467600-45475000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:45467600-45475000	Strong transcription	Brain Anterior Caudate	brain
50	chr1:45467600-45475200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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