Variant report

Variant	rs2168518
Chromosome Location	chr15:75081078-75081079
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	IRF4	chr15:75079607-75081355	GM12878	blood:	n/a	n/a
2	FOXM1	chr15:75079358-75081791	GM12878	blood:	n/a	n/a
3	NFYA	chr15:75080978-75081420	GM12878	blood:	n/a	n/a
4	CREB1	chr15:75079691-75081604	GM12878	blood:	n/a	n/a
5	TAF1	chr15:75080876-75081353	GM12892	blood:	n/a	n/a
6	YY1	chr15:75080821-75081562	GM12878	blood:	n/a	chr15:75081354-75081365
7	BCL3	chr15:75080954-75081570	GM12878	blood:	n/a	chr15:75081349-75081362
8	RELA	chr15:75079731-75081849	GM18526	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
9	BCLAF1	chr15:75079284-75082025	GM12878	blood:	n/a	chr15:75081349-75081362 chr15:75080342-75080351
10	RELA	chr15:75078968-75083276	GM18951	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
11	ATF2	chr15:75078945-75081778	GM12878	blood:	n/a	chr15:75079326-75079340
12	POLR2A	chr15:75077574-75083240	GM19193	blood:	n/a	n/a
13	NFATC1	chr15:75079098-75082965	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:75078871-75082774	GM12891	blood:	n/a	n/a
15	STAT3	chr15:75079696-75081648	GM12878	blood:	n/a	chr15:75081561-75081573
16	POLR2A	chr15:75078541-75083313	GM12892	blood:	n/a	n/a
17	ZBTB7A	chr15:75081045-75082020	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr15:75078876-75083272	GM12878	blood:	n/a	n/a
19	RELA	chr15:75078928-75083342	GM18505	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
20	EP300	chr15:75080830-75081614	GM12878	blood:	n/a	chr15:75081110-75081117
21	BHLHE40	chr15:75079621-75081908	GM12878	blood:	n/a	chr15:75081355-75081371
22	RELA	chr15:75079439-75082060	GM15510	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
23	POU2F2	chr15:75078933-75083247	GM12878	blood:	n/a	chr15:75081175-75081185 chr15:75081175-75081185 chr15:75081174-75081186 chr15:75081172-75081187 chr15:75081176-75081183 chr15:75081168-75081189 chr15:75081174-75081184 chr15:75081175-75081183 chr15:75081175-75081184 chr15:75081170-75081188 chr15:75081173-75081184
24	POLR2A	chr15:75078956-75083263	GM12892	blood:	n/a	n/a
25	CHD2	chr15:75079257-75083224	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:75079535-75083264	GM12878	blood:	n/a	n/a
27	YY1	chr15:75080824-75081579	GM12878	blood:	n/a	chr15:75081354-75081365
28	POLR2A	chr15:75076731-75083396	GM12892	blood:	n/a	n/a
29	PAX5	chr15:75080688-75081540	GM12878	blood:	n/a	n/a
30	BRCA1	chr15:75079767-75081462	GM12878	blood:	n/a	n/a
31	PAX5	chr15:75080984-75081562	GM12878	blood:	n/a	n/a
32	POLR2A	chr15:75072814-75083294	GM19099	blood:	n/a	n/a
33	POLR2A	chr15:75072482-75083351	GM12878	blood:	n/a	n/a
34	POU2F2	chr15:75079637-75081601	GM12878	blood:	n/a	chr15:75081175-75081185 chr15:75081175-75081185 chr15:75081174-75081186 chr15:75081172-75081187 chr15:75081176-75081183 chr15:75081168-75081189 chr15:75081174-75081184 chr15:75081175-75081183 chr15:75081175-75081184 chr15:75081170-75081188 chr15:75081173-75081184
35	CHD1	chr15:75079224-75081883	GM12878	blood:	n/a	n/a
36	POLR2A	chr15:75078570-75083275	GM18505	blood:	n/a	n/a
37	MAZ	chr15:75079154-75082852	GM12878	blood:	n/a	chr15:75082678-75082687 chr15:75081867-75081877
38	IKZF1	chr15:75080958-75081736	GM12878	blood:	n/a	chr15:75081414-75081422
39	BCLAF1	chr15:75078912-75083306	GM12878	blood:	n/a	chr15:75081349-75081362 chr15:75080342-75080351
40	YY1	chr15:75080891-75081298	GM12891	blood:	n/a	n/a
41	USF2	chr15:75080863-75081624	GM12878	blood:	n/a	chr15:75081355-75081371
42	PBX3	chr15:75081031-75081255	GM12878	blood:	n/a	n/a
43	BCL11A	chr15:75080681-75081558	GM12878	blood:	n/a	chr15:75081349-75081362
44	BCL11A	chr15:75080963-75081583	GM12878	blood:	n/a	chr15:75081349-75081362
45	ELF1	chr15:75079654-75081879	GM12878	blood:	n/a	chr15:75081109-75081120 chr15:75081109-75081120 chr15:75080344-75080357 chr15:75079925-75079938 chr15:75081110-75081119
46	MTA3	chr15:75078545-75083429	GM12878	blood:	n/a	n/a
47	RELA	chr15:75079339-75081560	GM12891	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
48	POLR2A	chr15:75078927-75082956	Raji	blood:	n/a	n/a
49	YY1	chr15:75080924-75081408	K562	blood:	n/a	chr15:75081354-75081365
50	EBF1	chr15:75078911-75082061	GM12878	blood:	n/a	chr15:75079866-75079877

No.	Distal block	Cell Line	Cell type
1	chr15:75080218..75087203-chr15:75106250..75113071,13	MCF-7	breast:
2	chr15:75079479..75082400-chr15:75103794..75106182,2	MCF-7	breast:
3	chr15:75080217..75082228-chr15:75182575..75184955,2	MCF-7	breast:
4	chr15:75079443..75082335-chr15:75197190..75199145,2	MCF-7	breast:
5	chr15:75079215..75085047-chr15:75133215..75137478,7	MCF-7	breast:
6	chr15:74906678..74909061-chr15:75078128..75081929,4	MCF-7	breast:
7	chr15:75079725..75083728-chr15:75089989..75095483,10	MCF-7	breast:

miRNA name	Chromosome Location	mirBase accession
hsa-miR-4513	chr15:75081064-75081085	MIMAT0019050

Variant related genes	Relation type
CSK	TF binding region
ENSG00000260919	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000261606	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11072507	0.88[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11072508	0.91[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072512	1.00[LWK][hapmap]
rs1127796	1.00[LWK][hapmap]
rs1133322	1.00[LWK][hapmap]
rs1133323	1.00[LWK][hapmap]
rs11630478	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630918	1.00[LWK][hapmap]
rs11632414	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633472	1.00[LWK][hapmap]
rs11635664	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636952	0.96[CEU][hapmap];0.85[MKK][hapmap]
rs11638130	1.00[LWK][hapmap]
rs11856413	1.00[LWK][hapmap]
rs12487	1.00[LWK][hapmap]
rs12591513	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594062	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898997	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901190	1.00[LWK][hapmap]
rs12903541	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12903896	0.87[AMR][1000 genomes]
rs12905199	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909307	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909335	1.00[LWK][hapmap]
rs12917376	0.94[ASN][1000 genomes]
rs1378940	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1378941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290573	1.00[LWK][hapmap]
rs2470890	0.89[ASW][hapmap];0.83[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2472304	0.83[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2960192	0.89[AMR][1000 genomes]
rs34862454	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35206230	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3765066	0.83[CEU][hapmap];0.87[MKK][hapmap]
rs3784789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62006566	0.80[AMR][1000 genomes]
rs62006567	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2168518	SCAMP2	cis	parietal	SCAN
rs2168518	STOML1	cis	parietal	SCAN
rs2168518	TMEM202	cis	parietal	SCAN
rs2168518	MPI	cis	lymphoblastoid	seeQTL
rs2168518	CSK	cis	lymphoblastoid	seeQTL
rs2168518	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs2168518	SCAMP5	cis	Artery Tibial	GTEx
rs2168518	SCAMP5	cis	cerebellum	SCAN
rs2168518	CPLX3	cis	parietal	SCAN
rs2168518	SCAMP5	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75075600-75083400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr15:75075800-75082000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr15:75076400-75082200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr15:75076400-75083200	Enhancers	Colon Smooth Muscle	Colon
5	chr15:75076400-75083400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr15:75076400-75083400	Genic enhancers	Fetal Stomach	stomach
7	chr15:75076400-75083400	Enhancers	Right Ventricle	heart
8	chr15:75076400-75084200	Enhancers	Spleen	Spleen
9	chr15:75076400-75085800	Enhancers	Left Ventricle	heart
10	chr15:75076600-75082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:75076600-75082600	Genic enhancers	NHEK	skin
12	chr15:75076600-75082800	Genic enhancers	Fetal Muscle Trunk	muscle
13	chr15:75076600-75083400	Enhancers	Right Atrium	heart
14	chr15:75076600-75083400	Enhancers	HMEC	breast
15	chr15:75076600-75084800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:75076800-75081600	Genic enhancers	Fetal Intestine Small	intestine
17	chr15:75076800-75083200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:75077200-75082200	Genic enhancers	Fetal Muscle Leg	muscle
19	chr15:75077600-75081800	Genic enhancers	Lung	lung
20	chr15:75077600-75083000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:75077600-75083000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:75077600-75083200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:75077800-75081200	Enhancers	Brain Substantia Nigra	brain
24	chr15:75077800-75082200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:75077800-75084400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:75077800-75092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:75078000-75081200	Enhancers	Liver	Liver
28	chr15:75078000-75081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:75078000-75082000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr15:75078000-75083400	Enhancers	Placenta	Placenta
31	chr15:75078000-75083400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr15:75078000-75083600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr15:75078000-75084200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr15:75078000-75085600	Enhancers	NHDF-Ad	bronchial
35	chr15:75078200-75081600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:75078200-75081600	Weak transcription	HUVEC	blood vessel
37	chr15:75078200-75082400	Enhancers	Brain Cingulate Gyrus	brain
38	chr15:75078200-75083200	Enhancers	Gastric	stomach
39	chr15:75078200-75083400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr15:75078200-75083600	Enhancers	Small Intestine	intestine
41	chr15:75078200-75084400	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr15:75078400-75081200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:75078400-75082000	Enhancers	Brain Anterior Caudate	brain
44	chr15:75078400-75082200	Enhancers	HSMM	muscle
45	chr15:75078600-75081200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr15:75078600-75082800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr15:75078600-75083000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr15:75078600-75083200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:75078600-75085000	Enhancers	NHLF	lung
50	chr15:75078800-75081200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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