Variant report

Variant	rs57242620
Chromosome Location	chr15:41046631-41046632
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr15:41046505-41048006	MCF-7	breast:	n/a	n/a
2	POLR2A	chr15:41046261-41047993	HepG2	liver:	n/a	n/a
3	YY1	chr15:41046619-41047818	HepG2	liver:	n/a	chr15:41047464-41047478 chr15:41047342-41047353 chr15:41047419-41047433 chr15:41047342-41047351 chr15:41047558-41047567
4	HCFC1	chr15:41046444-41048439	Hela-S3	cervix:	n/a	n/a
5	RUNX3	chr15:41046600-41046959	GM12878	blood:	n/a	n/a
6	YY1	chr15:41046606-41047051	GM12892	blood:	n/a	n/a
7	YY1	chr15:41046618-41047013	GM12878	blood:	n/a	n/a
8	MXI1	chr15:41046522-41048503	SK-N-SH	brain:	n/a	n/a
9	MAX	chr15:41046601-41047965	K562	blood:	n/a	n/a
10	MXI1	chr15:41046624-41047984	IMR90	lung:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41045818..41047338-chr15:41134388..41137195,2	MCF-7	breast:
2	chr15:41044630..41047663-chr15:41185217..41189065,4	K562	blood:
3	chr15:41046423..41049572-chr15:41185616..41187810,3	MCF-7	breast:
4	chr15:40986013..40988355-chr15:41045826..41048654,2	MCF-7	breast:
5	chr15:41045448..41048031-chr15:41068434..41070678,2	MCF-7	breast:
6	chr15:41045671..41048162-chr15:41135920..41137784,2	MCF-7	breast:
7	chr15:41042059..41049706-chr15:41053861..41061949,15	MCF-7	breast:
8	chr15:40731340..40734041-chr15:41045866..41047695,2	K562	blood:
9	chr15:41045813..41047463-chr15:41099042..41101691,3	K562	blood:
10	chr15:40987359..40990886-chr15:41044779..41048321,5	K562	blood:
11	chr15:41045748..41048901-chr15:41096709..41101394,9	K562	blood:
12	chr15:41036885..41040237-chr15:41045392..41049336,5	MCF-7	breast:
13	chr15:41045121..41047501-chr15:41186359..41188842,2	K562	blood:
14	chr15:41045965..41048868-chr15:41482776..41485356,2	K562	blood:
15	chr15:40984748..40990654-chr15:41044779..41050104,8	K562	blood:
16	chr15:41035271..41040468-chr15:41046040..41049485,6	MCF-7	breast:
17	chr15:41045896..41050408-chr15:41066208..41069896,5	MCF-7	breast:
18	chr15:40985310..40988262-chr15:41045857..41048554,2	MCF-7	breast:
19	chr15:40855952..40857673-chr15:41046204..41048687,2	K562	blood:

No data

Variant related genes	Relation type
RMDN3	TF binding region
ENSG00000051180	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000128891	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000240847	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000140320	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10220885	1.00[EUR][1000 genomes]
rs12323939	1.00[EUR][1000 genomes]
rs16971119	1.00[EUR][1000 genomes]
rs45501094	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45571032	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45604436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55896567	1.00[EUR][1000 genomes]
rs55906732	1.00[EUR][1000 genomes]
rs56229816	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57288992	1.00[EUR][1000 genomes]
rs58097169	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58375351	1.00[EUR][1000 genomes]
rs58681580	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58738238	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59508492	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59528823	1.00[EUR][1000 genomes]
rs59558714	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60109064	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60111609	1.00[EUR][1000 genomes]
rs60163307	1.00[EUR][1000 genomes]
rs60578270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60822673	1.00[EUR][1000 genomes]
rs6492962	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6492963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7161941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164574	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166733	1.00[EUR][1000 genomes]
rs7167831	1.00[EUR][1000 genomes]
rs7168217	1.00[EUR][1000 genomes]
rs7169273	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7171451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171898	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7172356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7178058	1.00[EUR][1000 genomes]
rs7178244	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182066	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182516	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011884	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011887	1.00[EUR][1000 genomes]
rs74011888	1.00[EUR][1000 genomes]
rs74011933	1.00[EUR][1000 genomes]
rs74011936	1.00[EUR][1000 genomes]
rs8035580	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8038751	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8039169	1.00[EUR][1000 genomes]
rs8039942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8040579	1.00[EUR][1000 genomes]
rs8040925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9672224	1.00[EUR][1000 genomes]
rs9744142	1.00[EUR][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	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41045800-41047000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:41045800-41047000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
3	chr15:41045800-41047000	Flanking Active TSS	Dnd41	blood
4	chr15:41045800-41047000	Flanking Active TSS	Hela-S3	cervix
5	chr15:41046000-41046800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:41046000-41046800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:41046000-41047000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:41046000-41047200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:41046000-41047800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:41046000-41047800	Active TSS	GM12878-XiMat	blood
11	chr15:41046200-41046800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr15:41046200-41046800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr15:41046200-41046800	Flanking Active TSS	Fetal Brain Female	brain
14	chr15:41046200-41047000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr15:41046200-41047000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr15:41046200-41047000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr15:41046200-41047000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:41046200-41047000	Flanking Active TSS	Fetal Thymus	thymus
19	chr15:41046200-41047200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr15:41046200-41047200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:41046200-41047200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr15:41046200-41047600	Active TSS	K562	blood
23	chr15:41046200-41047800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:41046200-41047800	Active TSS	HSMM	muscle
25	chr15:41046200-41048000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:41046200-41048000	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr15:41046200-41048200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr15:41046200-41048200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:41046200-41048200	Active TSS	Primary T cells from cord blood	blood
30	chr15:41046200-41048200	Active TSS	Muscle Satellite Cultured Cells	--
31	chr15:41046200-41048200	Active TSS	NHLF	lung
32	chr15:41046400-41046800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr15:41046400-41046800	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr15:41046400-41046800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr15:41046400-41047000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr15:41046400-41047000	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr15:41046400-41047000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr15:41046400-41047000	Flanking Active TSS	Placenta	Placenta
39	chr15:41046400-41047200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr15:41046400-41047600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:41046400-41047600	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr15:41046400-41047800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:41046400-41047800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:41046400-41047800	Active TSS	Fetal Intestine Large	intestine
45	chr15:41046400-41048000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:41046400-41048000	Active TSS	Colonic Mucosa	Colon
47	chr15:41046400-41048000	Active TSS	Rectal Smooth Muscle	rectum
48	chr15:41046400-41048000	Active TSS	Right Ventricle	heart
49	chr15:41046400-41048200	Active TSS	H1 Cell Line	embryonic stem cell
50	chr15:41046400-41048200	Active TSS	HUES64 Cell Line	embryonic stem cell

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