Variant report

Variant	rs9988654
Chromosome Location	chr1:45194500-45194501
allele	C/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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45103803..45106262-chr1:45193516..45195023,2	K562	blood:
2	chr1:45083155..45084917-chr1:45193474..45196151,2	MCF-7	breast:
3	chr1:45075313..45077004-chr1:45193857..45196108,2	K562	blood:
4	chr1:45190324..45200952-chr1:45272085..45288310,59	MCF-7	breast:
5	chr1:45194189..45198394-chr1:45270401..45277394,13	MCF-7	breast:
6	chr1:45193444..45198675-chr1:45475617..45480324,16	K562	blood:
7	chr1:45141360..45143507-chr1:45193675..45195240,2	MCF-7	breast:
8	chr1:45194156..45199355-chr1:45264282..45268731,9	MCF-7	breast:
9	chr1:45194369..45197773-chr1:46046767..46051199,5	K562	blood:
10	chr1:45193443..45200768-chr1:45280884..45289784,25	MCF-7	breast:
11	chr1:45193557..45198509-chr1:45202622..45207012,16	MCF-7	breast:
12	chr1:45194277..45197109-chr1:45476180..45479040,2	MCF-7	breast:
13	chr1:45193356..45196908-chr1:45277414..45280591,3	MCF-7	breast:
14	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
15	chr1:45193566..45196499-chr1:45246618..45248474,2	MCF-7	breast:
16	chr1:45194356..45196709-chr1:45671455..45674193,2	K562	blood:
17	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:
18	chr1:45194490..45196037-chr1:45552131..45554366,2	K562	blood:
19	chr1:45193581..45195151-chr1:46032484..46035467,2	K562	blood:
20	chr1:45193427..45195208-chr1:45196635..45198675,2	MCF-7	breast:
21	chr1:45193680..45198999-chr1:45768008..45771912,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000202444	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000187147	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10127580	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10127584	0.93[AFR][1000 genomes]
rs10127619	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10127899	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10127901	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1135319	0.83[AFR][1000 genomes]
rs56296258	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74070585	0.89[AFR][1000 genomes]
rs74070586	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74070587	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74070588	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
6	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
7	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
8	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

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45181200-45194800	Weak transcription	Brain Anterior Caudate	brain
2	chr1:45185600-45194800	Weak transcription	Dnd41	blood
3	chr1:45187800-45196200	Weak transcription	Right Atrium	heart
4	chr1:45188000-45195800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:45189400-45196200	Weak transcription	Brain Germinal Matrix	brain
6	chr1:45189400-45196200	Weak transcription	Colonic Mucosa	Colon
7	chr1:45189600-45195000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:45189800-45194800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:45189800-45195000	Weak transcription	Liver	Liver
10	chr1:45189800-45205000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:45190000-45194800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:45190200-45196000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:45190600-45196200	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:45190800-45194800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:45190800-45194800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:45190800-45195000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:45191000-45194800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:45191000-45195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:45191200-45194800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:45191200-45194800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:45191200-45194800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:45191200-45194800	Weak transcription	Thymus	Thymus
23	chr1:45191200-45196200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:45191400-45194800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:45191400-45194800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:45191400-45194800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:45191400-45194800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:45191400-45196600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:45192200-45196200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:45192600-45194800	Weak transcription	K562	blood
31	chr1:45192600-45196000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr1:45192600-45196200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:45192800-45194800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:45192800-45194800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:45192800-45194800	Weak transcription	A549	lung
36	chr1:45192800-45194800	Weak transcription	GM12878-XiMat	blood
37	chr1:45192800-45194800	Weak transcription	NHEK	skin
38	chr1:45192800-45195800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:45192800-45195800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:45192800-45195800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:45192800-45195800	Weak transcription	Placenta	Placenta
42	chr1:45192800-45195800	Weak transcription	HepG2	liver
43	chr1:45192800-45195800	Weak transcription	NH-A	brain
44	chr1:45192800-45195800	Weak transcription	NHDF-Ad	bronchial
45	chr1:45192800-45196200	Weak transcription	NHLF	lung
46	chr1:45192800-45196800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:45192800-45197200	Weak transcription	HSMM	muscle
48	chr1:45192800-45197600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:45192800-45198200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:45192800-45198800	Weak transcription	HMEC	breast

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