Variant report

Variant	rs690660
Chromosome Location	chr15:41139165-41139166
allele	A/G
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	RELA	chr15:41138997-41139938	GM18951	blood:	n/a	chr15:41139341-41139350 chr15:41139296-41139305 chr15:41139341-41139350 chr15:41139296-41139305
2	ELF1	chr15:41138887-41139349	GM12878	blood:	n/a	n/a
3	MTA3	chr15:41139095-41140080	GM12878	blood:	n/a	n/a
4	NFIC	chr15:41138989-41139473	GM12878	blood:	n/a	n/a
5	RELA	chr15:41139026-41139919	GM19099	blood:	n/a	chr15:41139341-41139350 chr15:41139296-41139305 chr15:41139341-41139350 chr15:41139296-41139305
6	POLR2A	chr15:41138971-41140028	GM12878	blood:	n/a	n/a
7	RELA	chr15:41139058-41139938	GM12878	blood:	n/a	chr15:41139341-41139350 chr15:41139296-41139305 chr15:41139341-41139350 chr15:41139296-41139305
8	TBP	chr15:41139160-41139902	GM12878	blood:	n/a	n/a
9	SMARCC1	chr15:41137762-41140084	Hela-S3	cervix:	n/a	chr15:41138241-41138250
10	BHLHE40	chr15:41139135-41139924	GM12878	blood:	n/a	n/a
11	EBF1	chr15:41138953-41139829	GM12878	blood:	n/a	chr15:41139188-41139199 chr15:41139188-41139201
12	RUNX3	chr15:41139126-41139935	GM12878	blood:	n/a	n/a
13	WRNIP1	chr15:41139023-41139976	GM12878	blood:	n/a	n/a
14	RELA	chr15:41139018-41139958	GM12891	blood:	n/a	chr15:41139341-41139350 chr15:41139296-41139305 chr15:41139341-41139350 chr15:41139296-41139305
15	PML	chr15:41139132-41139972	GM12878	blood:	n/a	n/a
16	ZNF143	chr15:41139134-41139873	GM12878	blood:	n/a	n/a
17	CTCF	chr15:41139060-41139210	GM12871	blood:	n/a	n/a
18	EBF1	chr15:41139013-41139467	GM12878	blood:	n/a	chr15:41139188-41139199 chr15:41139188-41139201
19	EBF1	chr15:41138989-41139393	GM12878	blood:	n/a	chr15:41139188-41139199 chr15:41139188-41139201
20	RELA	chr15:41138813-41139743	GM10847	blood:	n/a	chr15:41139341-41139350 chr15:41139296-41139305 chr15:41139341-41139350 chr15:41139296-41139305
21	EP300	chr15:41139091-41139864	GM12878	blood:	n/a	n/a
22	MTA3	chr15:41138863-41140107	GM12878	blood:	n/a	n/a
23	RUNX3	chr15:41139121-41140057	GM12878	blood:	n/a	n/a
24	RELA	chr15:41139141-41139877	GM19193	blood:	n/a	chr15:41139341-41139350 chr15:41139296-41139305 chr15:41139341-41139350 chr15:41139296-41139305

No.	Distal block	Cell Line	Cell type
1	chr15:41137977..41139735-chr15:41186627..41189501,2	MCF-7	breast:
2	chr15:41138287..41141935-chr15:41144190..41148215,5	MCF-7	breast:
3	chr15:41131773..41133919-chr15:41138481..41140259,2	MCF-7	breast:
4	chr15:41098633..41101215-chr15:41138030..41140092,3	K562	blood:
5	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
6	chr15:41135781..41139367-chr15:41195514..41200270,4	MCF-7	breast:
7	chr15:41137274..41141358-chr15:41148658..41151865,7	MCF-7	breast:
8	chr15:41135079..41139908-chr15:41161283..41167324,7	MCF-7	breast:
9	chr15:41137927..41140333-chr15:41154449..41156600,3	MCF-7	breast:
10	chr15:41134891..41137417-chr15:41138433..41142150,4	MCF-7	breast:
11	chr15:41135103..41140677-chr15:41182913..41189081,12	MCF-7	breast:
12	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261183	TF binding region
ENSG00000104140	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000166140	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11639292	0.98[EUR][1000 genomes]
rs2412569	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412570	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917953	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622538	0.98[EUR][1000 genomes]
rs659232	1.00[CHD][hapmap]
rs668708	0.87[EUR][1000 genomes]
rs668750	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680493	0.99[EUR][1000 genomes]
rs689589	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689594	1.00[CEU][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs689618	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689626	1.00[CHD][hapmap]
rs689733	0.86[EUR][1000 genomes]
rs689736	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690435	0.89[EUR][1000 genomes]
rs690572	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs690660	RP11-111A22.1	cis	Artery Tibial	GTEx
rs690660	ZFYVE19	cis	parietal	SCAN
rs690660	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs690660	ZFYVE19	cis	cerebellum	SCAN
rs690660	C15orf57	cis	Artery Tibial	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41135600-41140200	Active TSS	Rectal Smooth Muscle	rectum
2	chr15:41135600-41140400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:41136800-41139200	Enhancers	K562	blood
4	chr15:41136800-41140400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr15:41137000-41140800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
6	chr15:41137200-41139200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
7	chr15:41137200-41140200	Enhancers	Spleen	Spleen
8	chr15:41137400-41139400	Weak transcription	Primary T cells from cord blood	blood
9	chr15:41137400-41139600	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr15:41137400-41140000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:41137400-41140000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:41137400-41140000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr15:41137400-41140000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr15:41137400-41140200	Enhancers	Primary B cells from peripheral blood	blood
15	chr15:41137400-41152200	Weak transcription	Small Intestine	intestine
16	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
17	chr15:41137600-41139400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:41137600-41140200	Enhancers	Primary B cells from cord blood	blood
19	chr15:41137800-41140000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:41137800-41140000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr15:41137800-41140000	Flanking Active TSS	HMEC	breast
22	chr15:41137800-41140200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:41137800-41140200	Transcr. at gene 5' and 3'	NHEK	skin
24	chr15:41137800-41140400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr15:41137800-41140600	Enhancers	Primary hematopoietic stem cells	blood
26	chr15:41138000-41139200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr15:41138000-41139200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:41138000-41140400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:41138000-41140800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:41138000-41140800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:41138200-41139400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr15:41138200-41139600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr15:41138200-41140000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:41138400-41139200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr15:41138400-41139200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:41138400-41139600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:41138400-41140000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr15:41138400-41140000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:41138400-41140000	Flanking Active TSS	Stomach Mucosa	stomach
40	chr15:41138400-41140000	Enhancers	Thymus	Thymus
41	chr15:41138400-41140000	Flanking Active TSS	HepG2	liver
42	chr15:41138400-41140200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr15:41138400-41140200	Flanking Active TSS	Placenta	Placenta
44	chr15:41138600-41139200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr15:41138600-41139200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:41138600-41139200	Enhancers	Pancreas	Pancrea
47	chr15:41138600-41139400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr15:41138600-41139600	Flanking Active TSS	Colonic Mucosa	Colon
49	chr15:41138600-41139600	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr15:41138600-41139600	Bivalent Enhancer	Fetal Muscle Leg	muscle

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