Variant report

Variant	rs5030789
Chromosome Location	chr15:40986355-40986356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:49)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:49 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr15:40986312-40987561	GM12878	blood:	n/a	n/a
2	ETS1	chr15:40986168-40987937	GM12878	blood:	n/a	chr15:40987033-40987044
3	POLR2A	chr15:40986315-40987930	GM19193	blood:	n/a	n/a
4	MAX	chr15:40986214-40986456	GM12878	blood:	n/a	n/a
5	MTA3	chr15:40985866-40988075	GM12878	blood:	n/a	n/a
6	MAX	chr15:40986195-40988024	NB4	blood:	n/a	chr15:40988005-40988014
7	RELA	chr15:40986252-40988005	GM15510	blood:	n/a	n/a
8	BCLAF1	chr15:40986314-40987827	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:40986191-40987836	NB4	blood:	n/a	n/a
10	POLR2A	chr15:40986279-40987776	HepG2	liver:	n/a	n/a
11	SMARCB1	chr15:40986247-40988081	Hela-S3	cervix:	n/a	n/a
12	ZNF143	chr15:40986313-40987529	GM12878	blood:	n/a	chr15:40987032-40987042
13	CEBPB	chr15:40986305-40987010	GM12878	blood:	n/a	n/a
14	PML	chr15:40986011-40988106	GM12878	blood:	n/a	n/a
15	RUNX3	chr15:40986006-40988112	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:40986223-40987922	GM12892	blood:	n/a	n/a
17	NFIC	chr15:40986210-40987536	GM12878	blood:	n/a	n/a
18	MXI1	chr15:40986009-40988732	SK-N-SH	brain:	n/a	n/a
19	EP300	chr15:40986334-40987557	GM12878	blood:	n/a	n/a
20	MYC	chr15:40986226-40988082	NB4	blood:	n/a	chr15:40988005-40988014
21	POLR2A	chr15:40986336-40986359	K562	blood:	n/a	n/a
22	HCFC1	chr15:40985997-40988250	Hela-S3	cervix:	n/a	n/a
23	MAX	chr15:40986187-40988163	ECC-1	luminal epithelium:	n/a	chr15:40988005-40988014
24	STAT5A	chr15:40986071-40987941	GM12878	blood:	n/a	chr15:40986138-40986146
25	POLR2A	chr15:40986207-40987962	GM18505	blood:	n/a	n/a
26	POLR2A	chr15:40985951-40988075	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:40986065-40987912	Raji	blood:	n/a	n/a
28	POLR2A	chr15:40986171-40987923	GM18951	blood:	n/a	n/a
29	POLR2A	chr15:40986104-40987754	SK-N-MC	brain:	n/a	n/a
30	PAX5	chr15:40986128-40987176	GM12891	blood:	n/a	n/a
31	POLR2A	chr15:40986027-40987980	GM12892	blood:	n/a	n/a
32	PAX5	chr15:40985973-40987912	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:40986068-40988123	GM12891	blood:	n/a	n/a
34	PAX5	chr15:40986118-40987864	GM12878	blood:	n/a	n/a
35	PAX5	chr15:40986063-40987011	GM12878	blood:	n/a	n/a
36	JUN	chr15:40986111-40988138	K562	blood:	n/a	chr15:40987312-40987321
37	POLR2A	chr15:40986073-40987910	GM12892	blood:	n/a	n/a
38	TCF7L2	chr15:40986233-40988024	Hela-S3	cervix:	n/a	n/a
39	FOXM1	chr15:40986149-40987813	GM12878	blood:	n/a	n/a
40	RUNX3	chr15:40986025-40987917	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:40986069-40987624	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:40986174-40986419	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:40986121-40987987	GM12878	blood:	n/a	n/a
44	MXI1	chr15:40986215-40987990	GM12878	blood:	n/a	n/a
45	MAX	chr15:40986218-40988126	K562	blood:	n/a	chr15:40988005-40988014
46	CHD1	chr15:40986194-40987584	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:40986176-40987985	GM19099	blood:	n/a	n/a
48	MXI1	chr15:40986251-40988507	IMR90	lung:	n/a	n/a
49	CBX3	chr15:40986181-40988098	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:40985078..40988247-chr15:41185737..41188201,3	K562	blood:
2	chr15:40986013..40988355-chr15:41045826..41048654,2	MCF-7	breast:
3	chr15:40885583..40887494-chr15:40985320..40988301,2	K562	blood:
4	chr15:40985800..40990095-chr15:41055400..41057901,4	K562	blood:
5	chr15:40985310..40988262-chr15:41045857..41048554,2	MCF-7	breast:
6	chr15:40985736..40987452-chr15:41134754..41137017,2	MCF-7	breast:
7	chr15:40984748..40990654-chr15:41044779..41050104,8	K562	blood:
8	chr15:40954350..40957294-chr15:40985826..40987543,2	K562	blood:
9	chr15:40984748..40987218-chr15:41046649..41049070,3	K562	blood:

No data

Variant related genes	Relation type
RAD51	TF binding region
ENSG00000137880	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000137812	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10518697	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11070283	0.81[ASN][1000 genomes]
rs12148915	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442560	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591044	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592524	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903817	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12907442	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12908316	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12915636	0.89[ASN][1000 genomes]
rs17747423	0.89[ASN][1000 genomes]
rs17747633	0.89[ASN][1000 genomes]
rs1801321	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2619682	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28529389	0.81[ASN][1000 genomes]
rs28866515	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28891195	0.84[AMR][1000 genomes]
rs34305357	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34739056	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35127391	0.82[AMR][1000 genomes]
rs35684277	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4923880	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4924486	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4924492	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924496	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924498	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924502	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56409425	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59244061	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492964	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71471880	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7165509	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7175747	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7175905	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7176245	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176590	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7177265	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180135	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182499	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029530	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8036891	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8037180	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8038122	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8042386	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs957603	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920676	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv904100	chr15:40959624-40994706	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs5030789	RAD51	cis	multi-tissue	Pritchard
rs5030789	RP11-111A22.1	cis	Artery Tibial	GTEx
rs5030789	C15orf57	cis	Artery Aorta	GTEx
rs5030789	CCDC32	cis	multi-tissue	Pritchard
rs5030789	C15orf57	cis	Nerve Tibial	GTEx
rs5030789	RP11-111A22.1	cis	lung	GTEx
rs5030789	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs5030789	C15orf57	cis	lung	GTEx
rs5030789	C15orf57	cis	Stomach	GTEx
rs5030789	C15orf57	cis	Adipose Subcutaneous	GTEx
rs5030789	C15orf57	cis	Artery Tibial	GTEx
rs5030789	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs5030789	C15orf57	cis	Esophagus Muscularis	GTEx
rs5030789	C15orf57	cis	Muscle Skeletal	GTEx
rs5030789	C15orf57	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40984000-40986400	Weak transcription	Ovary	ovary
2	chr15:40985800-40986400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr15:40985800-40986400	Enhancers	Spleen	Spleen
4	chr15:40985800-40986400	Flanking Active TSS	Dnd41	blood
5	chr15:40985800-40986600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:40985800-40986800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr15:40985800-40986800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:40986000-40986400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:40986000-40986400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:40986000-40986400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr15:40986000-40986400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:40986000-40986400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:40986000-40986400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:40986000-40986400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:40986000-40986400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:40986000-40986400	Enhancers	Left Ventricle	heart
17	chr15:40986000-40986400	Enhancers	Small Intestine	intestine
18	chr15:40986000-40986400	Flanking Active TSS	HSMM	muscle
19	chr15:40986000-40986400	Flanking Active TSS	HSMMtube	muscle
20	chr15:40986000-40986400	Flanking Active TSS	K562	blood
21	chr15:40986000-40986400	Flanking Active TSS	NHEK	skin
22	chr15:40986000-40986400	Flanking Active TSS	NHLF	lung
23	chr15:40986000-40986400	Flanking Active TSS	Osteobl	bone
24	chr15:40986000-40986600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:40986000-40986600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:40986000-40986600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr15:40986000-40986600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:40986000-40986600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:40986000-40986600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:40986000-40986600	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr15:40986000-40986600	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr15:40986000-40986600	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr15:40986000-40986600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr15:40986000-40986600	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr15:40986000-40986600	Enhancers	Stomach Mucosa	stomach
36	chr15:40986000-40986600	Flanking Active TSS	Thymus	Thymus
37	chr15:40986000-40986600	Flanking Active TSS	HMEC	breast
38	chr15:40986000-40986600	Flanking Active TSS	HUVEC	blood vessel
39	chr15:40986000-40986600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr15:40986000-40986800	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr15:40986000-40986800	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr15:40986000-40986800	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr15:40986000-40986800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr15:40986000-40986800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:40986000-40986800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:40986000-40986800	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr15:40986000-40986800	Flanking Active TSS	Liver	Liver
48	chr15:40986000-40986800	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr15:40986000-40986800	Flanking Active TSS	Colonic Mucosa	Colon
50	chr15:40986000-40986800	Flanking Active TSS	Duodenum Mucosa	Duodenum

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