Variant report

Variant	rs1378942
Chromosome Location	chr15:75077367-75077368
allele	G/T
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:14)
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	SIN3A	chr15:75077193-75078324	GM12878	blood:	n/a	chr15:75078222-75078235
2	WRNIP1	chr15:75075080-75078241	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:75076731-75083396	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:75072814-75083294	GM19099	blood:	n/a	n/a
5	POLR2A	chr15:75072482-75083351	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:75074913-75078439	GM12878	blood:	n/a	n/a
7	NFIC	chr15:75076764-75077834	GM12878	blood:	n/a	n/a
8	MTA3	chr15:75074835-75078490	GM12878	blood:	n/a	n/a
9	PML	chr15:75075852-75078332	GM12878	blood:	n/a	n/a
10	BCLAF1	chr15:75077351-75078389	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:75072603-75078342	GM18505	blood:	n/a	n/a
12	POLR2A	chr15:75075481-75078388	GM12878	blood:	n/a	n/a
13	MTA3	chr15:75077119-75078320	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:75072699-75083327	GM12878	blood:	n/a	n/a
15	EBF1	chr15:75077071-75078399	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:75075052-75083417	GM12891	blood:	n/a	n/a
17	MXI1	chr15:75075571-75078430	GM12878	blood:	n/a	n/a
18	MAX	chr15:75075598-75077691	GM12878	blood:	n/a	chr15:75075992-75076005 chr15:75075994-75076003 chr15:75075994-75076004 chr15:75075993-75076004 chr15:75075992-75076005 chr15:75075993-75076003 chr15:75075993-75076004

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75073376..75079113-chr15:75130007..75137097,15	MCF-7	breast:
2	chr15:75043196..75045391-chr15:75075402..75077625,2	K562	blood:
3	chr15:75076309..75078257-chr15:75245859..75248166,2	K562	blood:
4	chr15:75075306..75077471-chr15:75113085..75115871,2	K562	blood:
5	chr15:75075890..75077943-chr15:75083927..75085940,3	K562	blood:
6	chr15:75072512..75079183-chr15:75180576..75186728,11	MCF-7	breast:
7	chr15:75073170..75080511-chr15:75126432..75130376,7	MCF-7	breast:
8	chr15:75074533..75077400-chr15:75247038..75249331,2	MCF-7	breast:
9	chr15:74927915..74930465-chr15:75075287..75077377,2	MCF-7	breast:
10	chr15:75074156..75079604-chr15:75107384..75112501,9	MCF-7	breast:
11	chr15:75072350..75078841-chr15:75107920..75114107,12	MCF-7	breast:
12	chr15:75069513..75071369-chr15:75076004..75078063,2	K562	blood:
13	chr15:74915721..74919302-chr15:75074662..75077539,3	MCF-7	breast:
14	chr15:75072261..75077453-chr15:75091040..75094267,5	K562	blood:

No data

Variant related genes	Relation type
CSK	TF binding region
ENSG00000178718	Chromatin interaction
ENSG00000179151	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11072507	0.88[CHB][hapmap];0.91[JPT][hapmap];0.90[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];0.94[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];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11632414	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633472	1.00[LWK][hapmap]
rs11635664	0.89[AFR][1000 genomes];0.93[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];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594062	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898997	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901190	1.00[LWK][hapmap]
rs12903541	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12903896	0.89[AMR][1000 genomes]
rs12905199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909307	0.89[AFR][1000 genomes];0.94[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];0.98[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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168518	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];0.89[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];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2960192	0.91[AMR][1000 genomes]
rs34862454	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35206230	1.00[AFR][1000 genomes];0.91[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];0.98[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62006567	0.85[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

Variant related diseases (count:4)

Disease	PMID	Source
Blood pressure	21909110	GWAS catalog
Diastolic blood pressure	21909115	GWAS catalog
Diastolic blood pressure	19430483	GWAS catalog
Systolic blood pressure	21909115	GWAS catalog

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1378942	SCAMP5	cis	Artery Tibial	GTEx
rs1378942	MPI	cis	lymphoblastoid	seeQTL
rs1378942	SCAMP5	cis	lung	GTEx
rs1378942	ULK3	cis	multi-tissue	Pritchard
rs1378942	SCAMP2	cis	parietal	SCAN
rs1378942	CPLX3	cis	parietal	SCAN
rs1378942	CSK	cis	lymphoblastoid	seeQTL
rs1378942	TMEM202	cis	parietal	SCAN
rs1378942	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs1378942	STOML1	cis	parietal	SCAN
rs1378942	SCAMP5	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75074800-75077400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:75075000-75077400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:75075000-75077600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr15:75075000-75077600	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr15:75075000-75077600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:75075000-75078200	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr15:75075000-75078400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:75075000-75078800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:75075200-75078200	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr15:75075600-75077400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr15:75075600-75077600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr15:75075600-75077600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
13	chr15:75075600-75080800	Enhancers	Fetal Heart	heart
14	chr15:75075600-75083400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr15:75075800-75078200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:75075800-75079600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
17	chr15:75075800-75082000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr15:75076000-75077800	Transcr. at gene 5' and 3'	Dnd41	blood
19	chr15:75076000-75079800	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr15:75076000-75080400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:75076000-75080600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:75076000-75080800	Enhancers	Fetal Brain Male	brain
23	chr15:75076200-75078200	Enhancers	Pancreas	Pancrea
24	chr15:75076200-75079400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
25	chr15:75076200-75080000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:75076200-75080000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:75076200-75080000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:75076200-75080200	Enhancers	Psoas Muscle	Psoas
29	chr15:75076200-75080200	Enhancers	Stomach Mucosa	stomach
30	chr15:75076400-75077600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:75076400-75077600	Active TSS	Rectal Smooth Muscle	rectum
32	chr15:75076400-75077600	Enhancers	Small Intestine	intestine
33	chr15:75076400-75077600	Enhancers	Osteobl	bone
34	chr15:75076400-75079200	Weak transcription	A549	lung
35	chr15:75076400-75079800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:75076400-75079800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:75076400-75080000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:75076400-75080000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:75076400-75082200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr15:75076400-75083200	Enhancers	Colon Smooth Muscle	Colon
41	chr15:75076400-75083400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr15:75076400-75083400	Genic enhancers	Fetal Stomach	stomach
43	chr15:75076400-75083400	Enhancers	Right Ventricle	heart
44	chr15:75076400-75084200	Enhancers	Spleen	Spleen
45	chr15:75076400-75085800	Enhancers	Left Ventricle	heart
46	chr15:75076600-75077400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:75076600-75077400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:75076600-75077600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:75076600-75077600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:75076600-75077600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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