Variant report

Variant	rs12910784
Chromosome Location	chr15:41039088-41039089
allele	A/C
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	SMC3	chr15:41038680-41039092	HepG2	liver:	n/a	chr15:41038859-41038873
2	CEBPB	chr15:41039077-41039383	ECC-1	luminal epithelium:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
3	TBL1XR1	chr15:41038777-41039472	K562	blood:	n/a	n/a
4	ZNF384	chr15:41038582-41039211	K562	blood:	n/a	n/a
5	CTCF	chr15:41038683-41039099	A549	lung:	n/a	chr15:41038859-41038880 chr15:41038860-41038873 chr15:41038857-41038875
6	EP300	chr15:41038669-41039451	K562	blood:	n/a	chr15:41039299-41039313 chr15:41038777-41038784
7	RAD21	chr15:41038729-41039125	A549	lung:	n/a	chr15:41038742-41038756 chr15:41038858-41038877
8	CEBPB	chr15:41038754-41039494	Hela-S3	cervix:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
9	ATF3	chr15:41039077-41039424	H1-hESC	embryonic stem cell:	n/a	n/a
10	CEBPB	chr15:41038910-41039402	A549	lung:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
11	CEBPB	chr15:41039019-41039492	IMR90	lung:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
12	CTCF	chr15:41038637-41039223	HCT-116	colon:	n/a	chr15:41038859-41038880 chr15:41038860-41038873 chr15:41038857-41038875
13	CEBPB	chr15:41038972-41039492	K562	blood:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
14	CEBPB	chr15:41038938-41039518	MCF-7	breast:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
15	JUND	chr15:41038689-41039526	K562	blood:	n/a	chr15:41039368-41039377
16	CTCF	chr15:41038763-41039180	HCT-116	colon:	n/a	chr15:41038859-41038880 chr15:41038860-41038873 chr15:41038857-41038875
17	RCOR1	chr15:41038718-41039595	K562	blood:	n/a	n/a
18	CEBPB	chr15:41038926-41039451	H1-hESC	embryonic stem cell:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
19	RAD21	chr15:41038662-41039102	A549	lung:	n/a	chr15:41038742-41038756 chr15:41038858-41038877
20	POLR2A	chr15:41038812-41039279	K562	blood:	n/a	n/a
21	CEBPB	chr15:41039015-41039460	HepG2	liver:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
22	CEBPB	chr15:41039085-41039463	K562	blood:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
23	SIN3AK20	chr15:41038615-41039221	MCF-7	breast:	n/a	n/a
24	CTCF	chr15:41038618-41039119	A549	lung:	n/a	chr15:41038859-41038880 chr15:41038860-41038873 chr15:41038857-41038875
25	CTCF	chr15:41038617-41039297	SK-N-SH	brain:	n/a	chr15:41038859-41038880 chr15:41038860-41038873 chr15:41038857-41038875
26	RCOR1	chr15:41038835-41039282	K562	blood:	n/a	n/a
27	POLR2A	chr15:41038695-41039790	U87	brain:	n/a	n/a
28	GATA1	chr15:41037682-41039421	PBDE	blood:	n/a	chr15:41037997-41038006 chr15:41037993-41038009 chr15:41038373-41038382 chr15:41037998-41038015 chr15:41038370-41038386 chr15:41038375-41038382 chr15:41038368-41038389 chr15:41038370-41038386 chr15:41038375-41038385
29	JUN	chr15:41038622-41040733	K562	blood:	n/a	chr15:41039368-41039377
30	CEBPB	chr15:41038843-41039511	K562	blood:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
31	RAD21	chr15:41038725-41039128	ECC-1	luminal epithelium:	n/a	chr15:41038742-41038756 chr15:41038858-41038877
32	ZC3H11A	chr15:41038783-41039290	K562	blood:	n/a	n/a
33	RAD21	chr15:41038621-41039208	HCT-116	colon:	n/a	chr15:41038742-41038756 chr15:41038858-41038877
34	RAD21	chr15:41038635-41039290	SK-N-SH	brain:	n/a	chr15:41038742-41038756 chr15:41038858-41038877
35	FOXA2	chr15:41038606-41039102	A549	lung:	n/a	n/a
36	RAD21	chr15:41038653-41039100	HepG2	liver:	n/a	chr15:41038742-41038756 chr15:41038858-41038877
37	CEBPB	chr15:41039069-41039458	ECC-1	luminal epithelium:	n/a	chr15:41039298-41039309 chr15:41039367-41039375
38	SMC3	chr15:41038647-41039714	SK-N-SH	brain:	n/a	chr15:41038859-41038873
39	CTCF	chr15:41038697-41039157	MCF-7	breast:	n/a	chr15:41038859-41038880 chr15:41038860-41038873 chr15:41038857-41038875
40	RAD21	chr15:41038717-41039113	HCT-116	colon:	n/a	chr15:41038742-41038756 chr15:41038858-41038877

No.	Distal block	Cell Line	Cell type
1	chr15:41031017..41033907-chr15:41037060..41039542,3	MCF-7	breast:
2	chr15:41038363..41039429-chr15:41074382..41075453,6	MCF-7	breast:
3	chr15:40986478..40988882-chr15:41036813..41039846,3	K562	blood:
4	chr15:41038391..41039742-chr15:41185999..41187256,5	K562	blood:
5	chr15:41036885..41040237-chr15:41045392..41049336,5	MCF-7	breast:
6	chr15:41038439..41039388-chr15:41150012..41150536,2	K562	blood:
7	chr15:41037589..41040458-chr15:41068418..41070751,2	K562	blood:
8	chr15:41035271..41040468-chr15:41046040..41049485,6	MCF-7	breast:
9	chr15:41038384..41039532-chr15:41074422..41075462,11	MCF-7	breast:
10	chr15:41038672..41039301-chr15:41186026..41186831,3	MCF-7	breast:
11	chr15:41036541..41039505-chr15:41136514..41138272,3	MCF-7	breast:

Variant related genes	Relation type
RMDN3	TF binding region
ENSG00000104142	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000051180	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 19 )

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

rs_ID	r²[population]
rs11070290	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12898552	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2010300	0.85[EUR][1000 genomes]
rs2289219	0.88[EUR][1000 genomes]
rs2304583	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412545	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2899000	0.82[EUR][1000 genomes]
rs34621344	0.84[EUR][1000 genomes]
rs34988257	0.87[EUR][1000 genomes]
rs36094699	0.81[AMR][1000 genomes]
rs3759796	0.85[EUR][1000 genomes]
rs45592734	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5030783	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62018584	0.81[EUR][1000 genomes]
rs62019934	0.80[AMR][1000 genomes]
rs8031427	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8038396	0.80[AMR][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	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
4	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
5	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

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12910784	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12910784	C15orf57	cis	Esophagus Mucosa	GTEx
rs12910784	RP11-111A22.1	cis	lung	GTEx
rs12910784	C15orf57	cis	lung	GTEx
rs12910784	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs12910784	C15orf57	cis	Nerve Tibial	GTEx
rs12910784	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12910784	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs12910784	C15orf57	cis	Artery Tibial	GTEx
rs12910784	CCDC32	cis	multi-tissue	Pritchard
rs12910784	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12910784	C15orf57	cis	Muscle Skeletal	GTEx
rs12910784	C15orf57	cis	Stomach	GTEx
rs12910784	RAD51	cis	multi-tissue	Pritchard
rs12910784	C15orf57	cis	Artery Aorta	GTEx
rs12910784	ZFYVE19	cis	multi-tissue	Pritchard
rs12910784	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12910784	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs12910784	C15orf57	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41008200-41046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:41019400-41046200	Strong transcription	Fetal Stomach	stomach
3	chr15:41020000-41043600	Strong transcription	Dnd41	blood
4	chr15:41020800-41045400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr15:41021800-41044600	Strong transcription	Brain Germinal Matrix	brain
6	chr15:41023200-41045200	Strong transcription	Thymus	Thymus
7	chr15:41023800-41045200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:41025600-41045000	Strong transcription	Primary T cells from cord blood	blood
9	chr15:41025600-41045400	Strong transcription	Stomach Smooth Muscle	stomach
10	chr15:41026000-41044600	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:41026200-41044600	Strong transcription	Lung	lung
12	chr15:41026800-41045200	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr15:41029000-41041800	Weak transcription	Fetal Kidney	kidney
14	chr15:41030800-41044000	Weak transcription	Psoas Muscle	Psoas
15	chr15:41031000-41046600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:41032000-41043000	Weak transcription	Fetal Brain Male	brain
17	chr15:41032600-41046200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:41032600-41046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:41032600-41046600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:41033200-41039200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:41033200-41042000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:41034200-41045800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr15:41034400-41044400	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:41034400-41044600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:41034400-41045200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:41034600-41044800	Strong transcription	Brain Substantia Nigra	brain
27	chr15:41034600-41045800	Genic enhancers	Fetal Intestine Small	intestine
28	chr15:41034800-41044400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr15:41034800-41044600	Strong transcription	Fetal Brain Female	brain
30	chr15:41034800-41046200	Genic enhancers	Fetal Intestine Large	intestine
31	chr15:41035600-41039800	Strong transcription	Ovary	ovary
32	chr15:41035600-41040600	Genic enhancers	K562	blood
33	chr15:41035800-41039800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:41035800-41046600	Weak transcription	Right Atrium	heart
35	chr15:41036000-41040400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr15:41036200-41041000	Strong transcription	Gastric	stomach
37	chr15:41036600-41040400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:41036600-41041600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:41036600-41042800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:41036600-41042800	Weak transcription	HSMMtube	muscle
41	chr15:41036600-41043000	Weak transcription	HMEC	breast
42	chr15:41036600-41044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr15:41036600-41045200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:41036600-41045400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:41036600-41045800	Weak transcription	NH-A	brain
46	chr15:41036800-41043800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr15:41036800-41044400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr15:41036800-41046000	Weak transcription	Fetal Heart	heart
49	chr15:41036800-41046200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:41037000-41041400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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