Variant report

Variant	rs12487
Chromosome Location	chr15:75136694-75136695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr15:75136099-75136701	MCF-7	breast:	n/a	n/a
2	POLR2A	chr15:75134600-75136938	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr15:75136230-75136819	GM12891	blood:	n/a	n/a
4	POLR2A	chr15:75136135-75137056	K562	blood:	n/a	n/a
5	MXI1	chr15:75134338-75137403	SK-N-SH	brain:	n/a	chr15:75135661-75135670 chr15:75135663-75135672
6	POLR2A	chr15:75136131-75136734	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:75136490-75136738	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:75134277-75136919	K562	blood:	n/a	n/a
9	POLR2A	chr15:75134803-75137136	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr15:75134883-75136922	GM12878	blood:	n/a	n/a
11	SIN3AK20	chr15:75134697-75136785	MCF-7	breast:	n/a	n/a
12	POLR2A	chr15:75134970-75137245	GM12892	blood:	n/a	n/a
13	POLR2A	chr15:75135274-75136775	GM12891	blood:	n/a	n/a
14	POLR2A	chr15:75134933-75137369	GM12892	blood:	n/a	n/a
15	POLR2A	chr15:75136116-75136833	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:75134964-75136985	K562	blood:	n/a	n/a
17	POLR2A	chr15:75134940-75136883	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr15:75134914-75136948	GM12892	blood:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75079215..75085047-chr15:75133215..75137478,7	MCF-7	breast:
2	chr15:74906653..74908395-chr15:75135147..75137390,2	K562	blood:
3	chr15:74906299..74909390-chr15:75133726..75137690,7	MCF-7	breast:
4	chr15:75135788..75137937-chr15:75174373..75175874,2	MCF-7	breast:
5	chr15:75118538..75120714-chr15:75135771..75139266,4	K562	blood:
6	chr15:75052835..75054344-chr15:75136259..75138062,2	K562	blood:
7	chr15:75105168..75109047-chr15:75134120..75137766,4	K562	blood:
8	chr15:75072228..75074857-chr15:75134119..75137193,5	K562	blood:
9	chr15:75133683..75136875-chr15:75181140..75184004,7	K562	blood:
10	chr15:75135715..75138276-chr15:75139819..75143025,6	K562	blood:
11	chr15:75135427..75140750-chr15:75141950..75147054,10	K562	blood:
12	chr15:75135967..75138215-chr15:75196939..75199387,3	K562	blood:
13	chr15:75090900..75093717-chr15:75134239..75137508,3	MCF-7	breast:
14	chr15:75133950..75137156-chr15:75180779..75184661,9	MCF-7	breast:
15	chr15:75135797..75138668-chr15:75143176..75146551,4	K562	blood:
16	chr15:75073376..75079113-chr15:75130007..75137097,15	MCF-7	breast:
17	chr15:75133790..75137554-chr15:75195204..75200578,14	MCF-7	breast:
18	chr15:75132595..75137581-chr15:75190842..75194074,4	K562	blood:
19	chr15:75134049..75139648-chr15:75161531..75167020,13	MCF-7	breast:
20	chr15:75136180..75138079-chr15:75161900..75164141,2	K562	blood:
21	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
22	chr15:75134794..75137581-chr15:75190842..75193156,3	K562	blood:
23	chr15:75135336..75137971-chr15:75192308..75194100,2	MCF-7	breast:
24	chr15:75131716..75139878-chr15:75227772..75233177,11	MCF-7	breast:
25	chr15:75072623..75074857-chr15:75134348..75137142,2	K562	blood:

No data

Variant related genes	Relation type
ULK3	TF binding region
ENSG00000140497	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000264386	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000260824	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000213578	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11072511	0.88[CEU][hapmap]
rs11072512	0.92[CEU][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap]
rs11072513	0.89[CEU][hapmap];0.88[CHB][hapmap]
rs11072514	0.89[CEU][hapmap];0.88[CHB][hapmap]
rs1127796	0.92[CEU][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap]
rs1130741	0.92[CEU][hapmap]
rs1133322	0.89[CEU][hapmap];1.00[LWK][hapmap]
rs1133323	0.84[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap]
rs11630918	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.88[MKK][hapmap];0.81[EUR][1000 genomes]
rs11633472	0.84[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap]
rs11638130	0.84[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap]
rs11854704	0.89[CEU][hapmap]
rs11856413	0.84[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap]
rs12901190	0.84[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap]
rs12909335	0.84[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap]
rs12917376	0.84[AMR][1000 genomes]
rs1378942	1.00[LWK][hapmap]
rs2168518	1.00[LWK][hapmap]
rs2290572	0.82[CEU][hapmap]
rs2290573	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2415251	0.84[CEU][hapmap]
rs3765066	0.83[MKK][hapmap]
rs3812945	0.86[ASW][hapmap]
rs4480762	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4886417	0.86[ASW][hapmap]
rs4886636	0.88[CEU][hapmap]
rs4886648	0.86[ASW][hapmap]
rs4886649	1.00[ASW][hapmap]
rs6495122	0.96[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs7495739	0.92[CEU][hapmap]
rs7497393	0.92[CEU][hapmap]

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	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers 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 miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv904382	chr15:75129594-75140854	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569992	chr15:75132319-75137868	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12487	CYP1A1	cis	cerebellum	SCAN
rs12487	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs12487	SCAMP5	cis	lung	GTEx
rs12487	SCAMP2	cis	Whole Blood	GTEx
rs12487	SCAMP2	cis	lymphoblastoid	seeQTL
rs12487	SCAMP5	cis	Artery Tibial	GTEx
rs12487	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12487	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs12487	SCAMP2	cis	parietal	SCAN
rs12487	ULK3	cis	parietal	SCAN
rs12487	ULK3	cis	multi-tissue	Pritchard
rs12487	MPI	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75135400-75136800	Enhancers	Primary B cells from cord blood	blood
2	chr15:75135400-75136800	Enhancers	Fetal Heart	heart
3	chr15:75135800-75136800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:75135800-75136800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:75135800-75137000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:75135800-75138200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr15:75135800-75138200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:75135800-75139800	Weak transcription	Small Intestine	intestine
9	chr15:75136000-75136800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:75136000-75136800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr15:75136000-75136800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:75136000-75136800	Enhancers	Brain Cingulate Gyrus	brain
13	chr15:75136000-75136800	Enhancers	Fetal Lung	lung
14	chr15:75136000-75136800	Weak transcription	Left Ventricle	heart
15	chr15:75136000-75136800	Genic enhancers	Rectal Mucosa Donor 31	rectum
16	chr15:75136000-75136800	Transcr. at gene 5' and 3'	Hela-S3	cervix
17	chr15:75136000-75137000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:75136000-75137000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:75136000-75137000	Genic enhancers	Fetal Intestine Small	intestine
20	chr15:75136000-75137000	Weak transcription	Lung	lung
21	chr15:75136000-75137200	Enhancers	Esophagus	oesophagus
22	chr15:75136000-75137800	Weak transcription	Aorta	Aorta
23	chr15:75136200-75136800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr15:75136200-75136800	Enhancers	Brain Germinal Matrix	brain
25	chr15:75136200-75136800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr15:75136200-75136800	Genic enhancers	Fetal Intestine Large	intestine
27	chr15:75136200-75136800	Genic enhancers	Rectal Mucosa Donor 29	rectum
28	chr15:75136200-75137000	Enhancers	H9 Cell Line	embryonic stem cell
29	chr15:75136200-75137000	Enhancers	Primary B cells from peripheral blood	blood
30	chr15:75136200-75137000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr15:75136200-75137000	Enhancers	Brain Anterior Caudate	brain
32	chr15:75136200-75137000	Genic enhancers	Fetal Stomach	stomach
33	chr15:75136200-75137000	Enhancers	Stomach Smooth Muscle	stomach
34	chr15:75136200-75137000	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr15:75136200-75137200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:75136200-75137200	Weak transcription	Fetal Brain Female	brain
37	chr15:75136200-75137400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr15:75136200-75137600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:75136200-75137600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:75136200-75138200	Genic enhancers	Fetal Thymus	thymus
41	chr15:75136200-75139600	Weak transcription	Stomach Mucosa	stomach
42	chr15:75136200-75140000	Weak transcription	Ovary	ovary
43	chr15:75136200-75144200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr15:75136200-75155800	Weak transcription	NH-A	brain
45	chr15:75136200-75160000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:75136200-75161800	Weak transcription	Fetal Kidney	kidney
47	chr15:75136400-75136800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:75136400-75136800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
49	chr15:75136400-75136800	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr15:75136400-75136800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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