Variant report

Variant	rs1383616
Chromosome Location	chr15:73929185-73929186
allele	G/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	MAX	chr15:73928694-73929283	HepG2	liver:	n/a	n/a
2	CTCF	chr15:73928612-73929217	K562	blood:	n/a	chr15:73928992-73929005 chr15:73928985-73929006 chr15:73928991-73929007 chr15:73928990-73929008 chr15:73928996-73929005 chr15:73928992-73929005 chr15:73928993-73929003
3	SMC3	chr15:73928716-73929245	Hela-S3	cervix:	n/a	chr15:73928992-73929006 chr15:73928992-73929002
4	BRCA1	chr15:73928902-73929212	HepG2	liver:	n/a	n/a
5	FOSL2	chr15:73928693-73929239	A549	lung:	n/a	n/a
6	RAD21	chr15:73928670-73929318	A549	lung:	n/a	chr15:73928991-73929004 chr15:73928992-73929002 chr15:73928988-73929007
7	MXI1	chr15:73928573-73929505	SK-N-SH	brain:	n/a	n/a
8	BCLAF1	chr15:73928795-73929208	GM12878	blood:	n/a	n/a
9	BHLHE40	chr15:73928787-73929270	GM12878	blood:	n/a	n/a
10	JUND	chr15:73928799-73929214	Hela-S3	cervix:	n/a	n/a
11	TEAD4	chr15:73928718-73929252	ECC-1	luminal epithelium:	n/a	n/a
12	BRCA1	chr15:73928783-73929336	Hela-S3	cervix:	n/a	n/a
13	MAX	chr15:73928790-73929194	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr15:73928732-73929231	IMR90	lung:	n/a	chr15:73928991-73929004 chr15:73928992-73929002 chr15:73928988-73929007
15	FOXA1	chr15:73928739-73929240	HepG2	liver:	n/a	n/a
16	SMC3	chr15:73928758-73929195	K562	blood:	n/a	chr15:73928992-73929006 chr15:73928992-73929002
17	STAT3	chr15:73928814-73929230	MCF10A-Er-Src	breast:	n/a	n/a
18	MAX	chr15:73928785-73929203	K562	blood:	n/a	n/a
19	EBF1	chr15:73928714-73929195	GM12878	blood:	n/a	n/a
20	CTCF	chr15:73928672-73929350	MCF-7	breast:	n/a	chr15:73928992-73929005 chr15:73928985-73929006 chr15:73928991-73929007 chr15:73928990-73929008 chr15:73928996-73929005 chr15:73928992-73929005 chr15:73928993-73929003
21	MYC	chr15:73928812-73929222	H1-hESC	embryonic stem cell:	n/a	n/a
22	RFX5	chr15:73928838-73929192	HepG2	liver:	n/a	n/a
23	RAD21	chr15:73928718-73929211	H1-hESC	embryonic stem cell:	n/a	chr15:73928991-73929004 chr15:73928992-73929002 chr15:73928988-73929007
24	CTCF	chr15:73928701-73929328	GM12878	blood:	n/a	chr15:73928992-73929005 chr15:73928985-73929006 chr15:73928991-73929007 chr15:73928990-73929008 chr15:73928996-73929005 chr15:73928992-73929005 chr15:73928993-73929003
25	NR3C1	chr15:73928790-73929296	A549	lung:	n/a	n/a
26	RAD21	chr15:73928748-73929291	A549	lung:	n/a	chr15:73928991-73929004 chr15:73928992-73929002 chr15:73928988-73929007
27	BHLHE40	chr15:73928817-73929316	HepG2	liver:	n/a	n/a
28	CTCF	chr15:73928662-73929201	HepG2	liver:	n/a	chr15:73928992-73929005 chr15:73928985-73929006 chr15:73928991-73929007 chr15:73928990-73929008 chr15:73928996-73929005 chr15:73928992-73929005 chr15:73928993-73929003
29	SMC3	chr15:73928732-73929325	GM12878	blood:	n/a	chr15:73928992-73929006 chr15:73928992-73929002
30	SP1	chr15:73928631-73929292	A549	lung:	n/a	n/a
31	CHD2	chr15:73928830-73929221	K562	blood:	n/a	n/a
32	WRNIP1	chr15:73928820-73929365	GM12878	blood:	n/a	n/a
33	GTF2F1	chr15:73928787-73929265	Hela-S3	cervix:	n/a	n/a
34	RAD21	chr15:73928700-73929226	SK-N-SH_RA	brain:	n/a	chr15:73928991-73929004 chr15:73928992-73929002 chr15:73928988-73929007
35	CTCF	chr15:73928761-73929193	ECC-1	luminal epithelium:	n/a	chr15:73928992-73929005 chr15:73928985-73929006 chr15:73928991-73929007 chr15:73928990-73929008 chr15:73928996-73929005 chr15:73928992-73929005 chr15:73928993-73929003
36	SMC3	chr15:73928547-73929521	SK-N-SH	brain:	n/a	chr15:73928992-73929006 chr15:73928992-73929002
37	SMC3	chr15:73928734-73929240	HepG2	liver:	n/a	chr15:73928992-73929006 chr15:73928992-73929002
38	FOS	chr15:73928818-73929223	MCF10A-Er-Src	breast:	n/a	n/a
39	JUND	chr15:73928844-73929219	HepG2	liver:	n/a	n/a
40	MAX	chr15:73928828-73929224	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr15:73928653-73929242	HepG2	liver:	n/a	chr15:73928991-73929004 chr15:73928992-73929002 chr15:73928988-73929007
42	BHLHE40	chr15:73928786-73929232	K562	blood:	n/a	n/a
43	TEAD4	chr15:73928742-73929246	H1-hESC	embryonic stem cell:	n/a	n/a
44	FOXM1	chr15:73928609-73929192	GM12878	blood:	n/a	n/a
45	TEAD4	chr15:73928764-73929265	HepG2	liver:	n/a	n/a
46	RAD21	chr15:73928736-73929251	ECC-1	luminal epithelium:	n/a	chr15:73928991-73929004 chr15:73928992-73929002 chr15:73928988-73929007
47	CTCF	chr15:73928706-73929211	K562	blood:	n/a	chr15:73928992-73929005 chr15:73928985-73929006 chr15:73928991-73929007 chr15:73928990-73929008 chr15:73928996-73929005 chr15:73928992-73929005 chr15:73928993-73929003
48	RAD21	chr15:73928728-73929319	MCF-7	breast:	n/a	chr15:73928991-73929004 chr15:73928992-73929002 chr15:73928988-73929007
49	TBP	chr15:73928797-73929200	GM12878	blood:	n/a	n/a
50	TCF12	chr15:73928555-73929314	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:73861467..73862464-chr15:73928634..73929400,4	MCF-7	breast:
2	chr15:73852547..73853537-chr15:73928518..73929514,5	K562	blood:
3	chr15:73886930..73887620-chr15:73928571..73929265,2	MCF-7	breast:
4	chr15:73921937..73932817-chr15:73973872..73983627,19	MCF-7	breast:
5	chr15:73928891..73929975-chr15:73969289..73970101,4	K562	blood:
6	chr15:73928631..73929310-chr15:73976806..73977438,2	MCF-7	breast:
7	chr15:73928442..73929397-chr15:73996956..73997684,2	MCF-7	breast:
8	chr15:73928211..73929721-chr15:73969066..73971811,2	MCF-7	breast:
9	chr15:73928417..73929456-chr15:73991468..73993254,16	MCF-7	breast:
10	chr15:73928404..73929624-chr15:73992333..73993300,6	K562	blood:
11	chr15:73928516..73929307-chr15:73996863..73997693,3	K562	blood:
12	chr15:73852770..73853342-chr15:73928816..73929372,2	MCF-7	breast:
13	chr15:73893982..73894748-chr15:73928565..73929402,2	MCF-7	breast:
14	chr15:73852575..73853414-chr15:73928105..73929408,6	MCF-7	breast:
15	chr15:73928462..73929402-chr15:73992230..73993688,9	MCF-7	breast:
16	chr15:73597949..73598920-chr15:73928445..73929381,7	MCF-7	breast:

Variant related genes	Relation type
NPTN	TF binding region
ENSG00000103855	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10851863	0.81[EUR][1000 genomes]
rs11072428	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072429	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072430	0.83[MEX][hapmap]
rs12148532	0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12148719	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12185108	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593246	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1481088	0.82[ASN][1000 genomes]
rs1481089	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16958079	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743500	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470111	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6495069	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6495076	0.81[JPT][hapmap]
rs7169374	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176654	0.91[MEX][hapmap]
rs8023823	0.91[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8028089	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8036954	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs8037836	0.87[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs899981	0.81[TSI][hapmap]
rs922687	0.84[ASN][1000 genomes]
rs9920359	0.83[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1383616	TLE3	cis	parietal	SCAN
rs1383616	ARIH1	cis	cerebellum	SCAN
rs1383616	FEZ1	trans	lymphoblastoid	seeQTL
rs1383616	NPTN	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73926400-73929200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:73926600-73929200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:73926600-73929600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:73926600-73930000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:73926600-73930000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:73926600-73931400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:73926800-73929600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:73926800-73930400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:73927000-73929200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:73927000-73931600	Weak transcription	Placenta	Placenta
11	chr15:73927200-73929400	Weak transcription	Fetal Intestine Small	intestine
12	chr15:73927200-73929400	Enhancers	HepG2	liver
13	chr15:73927400-73929200	Weak transcription	Osteobl	bone
14	chr15:73927400-73932200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:73927800-73929200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:73927800-73929200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:73927800-73929200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:73927800-73929200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:73928000-73929200	Weak transcription	HMEC	breast
20	chr15:73928600-73929200	Enhancers	Primary B cells from peripheral blood	blood
21	chr15:73928600-73929200	Active TSS	A549	lung
22	chr15:73928600-73930400	Enhancers	Fetal Intestine Large	intestine
23	chr15:73928600-73931400	Enhancers	GM12878-XiMat	blood
24	chr15:73928800-73929200	Enhancers	Fetal Kidney	kidney
25	chr15:73928800-73930400	Enhancers	NHEK	skin
26	chr15:73928800-73930800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:73929000-73929200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr15:73929000-73929200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr15:73929000-73929200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr15:73929000-73929200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr15:73929000-73929200	Enhancers	HUVEC	blood vessel
32	chr15:73929000-73929200	Enhancers	NHDF-Ad	bronchial
33	chr15:73929000-73929400	Enhancers	Hela-S3	cervix
34	chr15:73929000-73929600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr15:73929000-73929600	Weak transcription	NH-A	brain
36	chr15:73929000-73929800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:73929000-73930000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr15:73929000-73930200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:73929000-73930400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:73929000-73930400	Enhancers	Muscle Satellite Cultured Cells	--

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