Variant report

Variant	rs7169273
Chromosome Location	chr15:41047341-41047342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr15:41047261-41047985	Hela-S3	cervix:	n/a	n/a
2	MYC	chr15:41047261-41047831	A549	lung:	n/a	n/a
3	SP4	chr15:41047236-41047915	H1-hESC	embryonic stem cell:	n/a	chr15:41047518-41047529 chr15:41047541-41047557 chr15:41047516-41047532
4	SIN3AK20	chr15:41047255-41047705	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr15:41047194-41047918	K562	blood:	n/a	n/a
6	TAF1	chr15:41047036-41047896	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr15:41047197-41047908	K562	blood:	n/a	n/a
8	HDAC2	chr15:41047266-41047730	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:41047202-41047875	A549	lung:	n/a	n/a
10	YY1	chr15:41047170-41047755	SK-N-SH	brain:	n/a	chr15:41047464-41047478 chr15:41047342-41047353 chr15:41047419-41047433 chr15:41047342-41047351 chr15:41047558-41047567
11	MYC	chr15:41047266-41047752	MCF-7	breast:	n/a	n/a
12	FOXP2	chr15:41047263-41047801	PFSK-1	brain:	n/a	n/a
13	TCF3	chr15:41047326-41047562	GM12878	blood:	n/a	chr15:41047465-41047478
14	SIN3AK20	chr15:41046505-41048006	MCF-7	breast:	n/a	n/a
15	MAX	chr15:41047184-41047834	K562	blood:	n/a	n/a
16	BRCA1	chr15:41047283-41047638	HepG2	liver:	n/a	n/a
17	RAD21	chr15:41047265-41047861	H1-hESC	embryonic stem cell:	n/a	chr15:41047415-41047429
18	POLR2A	chr15:41047234-41047801	A549	lung:	n/a	n/a
19	TCF12	chr15:41046959-41047995	ECC-1	luminal epithelium:	n/a	n/a
20	CREB1	chr15:41046994-41047867	K562	blood:	n/a	chr15:41047449-41047462
21	STAT5A	chr15:41047246-41047858	K562	blood:	n/a	n/a
22	MAX	chr15:41047047-41047978	HCT-116	colon:	n/a	n/a
23	SRF	chr15:41047092-41047906	HCT-116	colon:	n/a	chr15:41047515-41047525
24	SRF	chr15:41047321-41047588	HepG2	liver:	n/a	chr15:41047515-41047525
25	NR2F2	chr15:41047326-41047871	K562	blood:	n/a	n/a
26	YY1	chr15:41047189-41047902	H1-hESC	embryonic stem cell:	n/a	chr15:41047464-41047478 chr15:41047342-41047353 chr15:41047419-41047433 chr15:41047342-41047351 chr15:41047558-41047567
27	USF1	chr15:41047324-41047644	A549	lung:	n/a	chr15:41047464-41047480 chr15:41047417-41047433
28	POLR2A	chr15:41047228-41047924	K562	blood:	n/a	n/a
29	ATF3	chr15:41047326-41047646	H1-hESC	embryonic stem cell:	n/a	chr15:41047452-41047459 chr15:41047451-41047462 chr15:41047449-41047459 chr15:41047450-41047461 chr15:41047451-41047459 chr15:41047449-41047462 chr15:41047449-41047459 chr15:41047448-41047463 chr15:41047449-41047462 chr15:41047450-41047461
30	ETS1	chr15:41047238-41047842	GM12878	blood:	n/a	chr15:41047265-41047278
31	POLR2A	chr15:41047240-41047780	A549	lung:	n/a	n/a
32	ZNF143	chr15:41047223-41047777	Hela-S3	cervix:	n/a	n/a
33	SIN3AK20	chr15:41046723-41047926	PANC-1	pancreas:	n/a	n/a
34	USF1	chr15:41047340-41047612	HepG2	liver:	n/a	chr15:41047464-41047480 chr15:41047417-41047433
35	POLR2A	chr15:41047179-41048399	K562	blood:	n/a	n/a
36	MAX	chr15:41047212-41047958	H1-hESC	embryonic stem cell:	n/a	n/a
37	EP300	chr15:41047312-41048101	GM12878	blood:	n/a	chr15:41047419-41047435 chr15:41047511-41047520 chr15:41047559-41047568
38	MAZ	chr15:41047082-41047807	GM12878	blood:	n/a	n/a
39	JUND	chr15:41047311-41047734	HepG2	liver:	n/a	chr15:41047451-41047460
40	POLR2A	chr15:41047192-41048000	GM12892	blood:	n/a	n/a
41	GTF2F1	chr15:41047337-41047962	K562	blood:	n/a	n/a
42	POLR2A	chr15:41047193-41047882	GM18526	blood:	n/a	n/a
43	POLR2A	chr15:41047204-41047889	GM12878	blood:	n/a	n/a
44	SIN3AK20	chr15:41047155-41047815	SK-N-SH	brain:	n/a	n/a
45	TAF1	chr15:41047277-41047834	GM12891	blood:	n/a	n/a
46	ZEB1	chr15:41047248-41047893	GM12878	blood:	n/a	n/a
47	USF1	chr15:41047235-41047852	ECC-1	luminal epithelium:	n/a	chr15:41047464-41047480 chr15:41047417-41047433
48	ELF1	chr15:41047250-41047744	K562	blood:	n/a	n/a
49	MYC	chr15:41046947-41048267	K562	blood:	n/a	n/a
50	RUNX3	chr15:41047143-41047856	GM12878	blood:	n/a	chr15:41047293-41047308 chr15:41047300-41047309

No.	Distal block	Cell Line	Cell type
1	chr15:41044630..41047663-chr15:41185217..41189065,4	K562	blood:
2	chr15:41046423..41049572-chr15:41185616..41187810,3	MCF-7	breast:
3	chr15:41046641..41048842-chr15:41243931..41246219,2	K562	blood:
4	chr15:40986013..40988355-chr15:41045826..41048654,2	MCF-7	breast:
5	chr15:40984748..40987218-chr15:41046649..41049070,3	K562	blood:
6	chr15:41045448..41048031-chr15:41068434..41070678,2	MCF-7	breast:
7	chr15:41045671..41048162-chr15:41135920..41137784,2	MCF-7	breast:
8	chr11:62622444..62623050-chr15:41047239..41048031,2	Hela-S3	cervix:
9	chr15:41042059..41049706-chr15:41053861..41061949,15	MCF-7	breast:
10	chr15:40731340..40734041-chr15:41045866..41047695,2	K562	blood:
11	chr15:41045813..41047463-chr15:41099042..41101691,3	K562	blood:
12	chr15:40987359..40990886-chr15:41044779..41048321,5	K562	blood:
13	chr15:41045748..41048901-chr15:41096709..41101394,9	K562	blood:
14	chr15:41036885..41040237-chr15:41045392..41049336,5	MCF-7	breast:
15	chr15:41045121..41047501-chr15:41186359..41188842,2	K562	blood:
16	chr15:41045965..41048868-chr15:41482776..41485356,2	K562	blood:
17	chr15:40984748..40990654-chr15:41044779..41050104,8	K562	blood:
18	chr15:41035271..41040468-chr15:41046040..41049485,6	MCF-7	breast:
19	chr15:41045896..41050408-chr15:41066208..41069896,5	MCF-7	breast:
20	chr12:56121964..56122628-chr15:41047145..41047901,2	Hela-S3	cervix:
21	chr15:40985310..40988262-chr15:41045857..41048554,2	MCF-7	breast:
22	chr15:41047268..41048047-chr2:46926297..46927002,2	Hela-S3	cervix:
23	chr15:41030963..41032960-chr15:41046925..41048677,2	K562	blood:
24	chr15:40855952..40857673-chr15:41046204..41048687,2	K562	blood:
25	chr12:57118473..57119279-chr15:41047161..41047984,2	Hela-S3	cervix:

Variant related genes	Relation type
RMDN3	TF binding region
ENSG00000240847	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000128965	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000171150	Chromatin interaction
ENSG00000128891	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000140320	Chromatin interaction

Extended variants
information (count: 58 )
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	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs45571032	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs45604436	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55896567	1.00[EUR][1000 genomes]
rs55906732	1.00[EUR][1000 genomes]
rs56229816	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57242620	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57288992	1.00[EUR][1000 genomes]
rs58097169	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58375351	1.00[EUR][1000 genomes]
rs58681580	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58738238	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59508492	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59528823	1.00[EUR][1000 genomes]
rs59558714	1.00[EUR][1000 genomes]
rs60109064	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60111609	1.00[EUR][1000 genomes]
rs60163307	1.00[EUR][1000 genomes]
rs60578270	1.00[EUR][1000 genomes]
rs60822673	1.00[EUR][1000 genomes]
rs6492962	0.89[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6492963	1.00[EUR][1000 genomes]
rs7161941	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7164574	1.00[EUR][1000 genomes]
rs7166733	1.00[EUR][1000 genomes]
rs7167831	1.00[EUR][1000 genomes]
rs7168217	1.00[EUR][1000 genomes]
rs7171451	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7171898	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7172356	0.92[LWK][hapmap];0.83[MKK][hapmap];1.00[EUR][1000 genomes]
rs7178058	1.00[EUR][1000 genomes]
rs7178244	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7182066	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7182516	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74011880	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74011881	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74011884	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74011886	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	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8038751	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8039169	1.00[EUR][1000 genomes]
rs8039942	1.00[EUR][1000 genomes]
rs8040579	1.00[EUR][1000 genomes]
rs8040925	1.00[EUR][1000 genomes]
rs9672224	1.00[EUR][1000 genomes]
rs9744142	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 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	chr15:41046000-41047800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr15:41046000-41047800	Active TSS	GM12878-XiMat	blood
3	chr15:41046200-41047600	Active TSS	K562	blood
4	chr15:41046200-41047800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:41046200-41047800	Active TSS	HSMM	muscle
6	chr15:41046200-41048000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:41046200-41048000	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr15:41046200-41048200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:41046200-41048200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:41046200-41048200	Active TSS	Primary T cells from cord blood	blood
11	chr15:41046200-41048200	Active TSS	Muscle Satellite Cultured Cells	--
12	chr15:41046200-41048200	Active TSS	NHLF	lung
13	chr15:41046400-41047600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:41046400-41047600	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr15:41046400-41047800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:41046400-41047800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:41046400-41047800	Active TSS	Fetal Intestine Large	intestine
18	chr15:41046400-41048000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:41046400-41048000	Active TSS	Colonic Mucosa	Colon
20	chr15:41046400-41048000	Active TSS	Rectal Smooth Muscle	rectum
21	chr15:41046400-41048000	Active TSS	Right Ventricle	heart
22	chr15:41046400-41048200	Active TSS	H1 Cell Line	embryonic stem cell
23	chr15:41046400-41048200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr15:41046400-41048200	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr15:41046400-41048200	Active TSS	A549	lung
26	chr15:41046600-41047400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:41046600-41047600	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr15:41046600-41047600	Active TSS	NH-A	brain
29	chr15:41046600-41047800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr15:41046600-41047800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:41046600-41047800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:41046600-41047800	Active TSS	Gastric	stomach
33	chr15:41046600-41047800	Bivalent/Poised TSS	HepG2	liver
34	chr15:41046600-41047800	Active TSS	NHEK	skin
35	chr15:41046600-41048000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr15:41046600-41048000	Active TSS	H9 Cell Line	embryonic stem cell
37	chr15:41046600-41048000	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr15:41046600-41048000	Active TSS	Aorta	Aorta
39	chr15:41046600-41048000	Active TSS	Colon Smooth Muscle	Colon
40	chr15:41046600-41048000	Active TSS	Ovary	ovary
41	chr15:41046600-41048000	Active TSS	Psoas Muscle	Psoas
42	chr15:41046600-41048000	Active TSS	Right Atrium	heart
43	chr15:41046600-41048000	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr15:41046600-41048000	Active TSS	Stomach Mucosa	stomach
45	chr15:41046600-41048000	Active TSS	HSMMtube	muscle
46	chr15:41046600-41048200	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr15:41046600-41048200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr15:41046600-41048200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:41046600-41048200	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr15:41046600-41048200	Flanking Active TSS	Primary hematopoietic stem cells	blood

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