Variant report

Variant	rs1918310
Chromosome Location	chr15:42065253-42065254
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	CTCF	chr15:42064685-42065680	SK-N-SH	brain:	n/a	n/a
2	MYC	chr15:42064973-42065532	K562	blood:	n/a	chr15:42065312-42065323 chr15:42065312-42065322 chr15:42065311-42065324 chr15:42065314-42065321 chr15:42065313-42065322 chr15:42065313-42065322 chr15:42065311-42065324 chr15:42065361-42065370 chr15:42065311-42065324 chr15:42065311-42065324 chr15:42065313-42065323 chr15:42065312-42065323
3	CTCF	chr15:42064884-42065330	HepG2	liver:	n/a	n/a
4	RAD21	chr15:42064716-42065533	SK-N-SH	brain:	n/a	n/a
5	SMC3	chr15:42064931-42065725	HepG2	liver:	n/a	n/a
6	CTCF	chr15:42064908-42065435	IMR90	lung:	n/a	n/a
7	POLR2A	chr15:42064869-42065759	PANC-1	pancreas:	n/a	n/a
8	CTCF	chr15:42064915-42065292	K562	blood:	n/a	n/a
9	USF2	chr15:42064904-42065347	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr15:42064840-42065495	A549	lung:	n/a	n/a
11	POLR2A	chr15:42065246-42065259	MCF10A-Er-Src	breast:	n/a	n/a
12	GATA3	chr15:42064949-42065335	SH-SY5Y	brain:	n/a	n/a
13	PML	chr15:42064831-42067236	GM12878	blood:	n/a	n/a
14	RAD21	chr15:42064846-42065461	ECC-1	luminal epithelium:	n/a	n/a
15	CTCF	chr15:42064994-42065257	HepG2	liver:	n/a	n/a
16	MAZ	chr15:42064970-42065318	K562	blood:	n/a	n/a
17	WRNIP1	chr15:42064992-42065267	GM12878	blood:	n/a	n/a
18	ZNF384	chr15:42064854-42065283	K562	blood:	n/a	n/a
19	MAX	chr15:42064966-42065282	K562	blood:	n/a	n/a
20	RAD21	chr15:42064895-42065390	GM12878	blood:	n/a	n/a
21	RAD21	chr15:42064850-42065437	HepG2	liver:	n/a	n/a
22	STAT5A	chr15:42064918-42065266	GM12878	blood:	n/a	n/a
23	RAD21	chr15:42064918-42065334	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr15:42064850-42065367	A549	lung:	n/a	n/a
25	RAD21	chr15:42064910-42065340	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZNF143	chr15:42064984-42065286	H1-hESC	embryonic stem cell:	n/a	n/a
27	FOXM1	chr15:42064874-42065338	GM12878	blood:	n/a	n/a
28	RAD21	chr15:42064899-42065489	IMR90	lung:	n/a	n/a
29	MAX	chr15:42064909-42065505	K562	blood:	n/a	chr15:42065312-42065323 chr15:42065312-42065322 chr15:42065311-42065324 chr15:42065314-42065321 chr15:42065313-42065322 chr15:42065313-42065322 chr15:42065311-42065324 chr15:42065361-42065370 chr15:42065311-42065324 chr15:42065311-42065324 chr15:42065313-42065323 chr15:42065312-42065323
30	CTCF	chr15:42064909-42065408	MCF-7	breast:	n/a	n/a
31	POLR2A	chr15:42065123-42067216	GM12878	blood:	n/a	n/a
32	CTCF	chr15:42064940-42065292	K562	blood:	n/a	n/a
33	CTCF	chr15:42064939-42065327	K562	blood:	n/a	n/a
34	POLR2A	chr15:42064944-42067574	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr15:42064891-42065324	K562	blood:	n/a	n/a
36	BRCA1	chr15:42064957-42065260	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr15:42064832-42065339	A549	lung:	n/a	n/a
38	RAD21	chr15:42064760-42065510	HCT-116	colon:	n/a	n/a
39	POLR2A	chr15:42064870-42065500	HepG2	liver:	n/a	n/a
40	BCLAF1	chr15:42064877-42065387	GM12878	blood:	n/a	n/a
41	RAD21	chr15:42064950-42065319	GM12878	blood:	n/a	n/a
42	MXI1	chr15:42064792-42067721	IMR90	lung:	n/a	chr15:42067063-42067078
43	POLR2A	chr15:42064912-42065262	K562	blood:	n/a	n/a
44	CTCF	chr15:42064898-42065327	MCF-7	breast:	n/a	n/a
45	RAD21	chr15:42064913-42065335	SK-N-SH_RA	brain:	n/a	n/a
46	MAX	chr15:42064921-42065493	NB4	blood:	n/a	chr15:42065312-42065323 chr15:42065312-42065322 chr15:42065311-42065324 chr15:42065314-42065321 chr15:42065313-42065322 chr15:42065313-42065322 chr15:42065311-42065324 chr15:42065361-42065370 chr15:42065311-42065324 chr15:42065311-42065324 chr15:42065313-42065323 chr15:42065312-42065323
47	MYC	chr15:42065022-42065256	H1-hESC	embryonic stem cell:	n/a	n/a
48	RAD21	chr15:42064890-42065388	HepG2	liver:	n/a	n/a
49	CTCF	chr15:42064786-42065429	HCT-116	colon:	n/a	n/a
50	RAD21	chr15:42064847-42065354	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42064035..42067811-chr15:42102222..42105290,4	K562	blood:
2	chr15:42063685..42066999-chr15:42102378..42105267,3	MCF-7	breast:
3	chr15:42010789..42012329-chr15:42064397..42066596,2	K562	blood:
4	chr15:41851361..41854178-chr15:42065182..42067599,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPTBN5-2	chr15:42064707-42065278	ENSG00000246549

Variant related genes	Relation type
MAPKBP1	TF binding region
ENSG00000260814	TF binding region
ENSG00000270702	Chromatin interaction
ENSG00000092445	Chromatin interaction
ENSG00000137802	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1105881	0.96[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1107858	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11632424	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11634956	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11635067	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11635415	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12440747	0.96[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12441300	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1531140	0.92[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16952372	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs16971976	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17676742	0.96[CEU][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap]
rs17677199	0.96[CEU][hapmap];0.92[JPT][hapmap]
rs17677991	0.96[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17678138	0.96[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17678552	0.96[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17678767	0.96[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17734856	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241522	0.92[CEU][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2277535	0.92[CEU][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2303516	0.92[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2303518	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2305654	0.92[CEU][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2412641	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2577960	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28373318	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28401754	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28432037	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28451764	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28680296	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28701757	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28754734	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3179542	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3743024	0.92[CEU][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3959569	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4923905	0.96[CEU][hapmap];0.92[JPT][hapmap]
rs4923910	0.83[EUR][1000 genomes]
rs4923914	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4923915	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4923919	0.82[YRI][hapmap]
rs4924570	0.86[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap]
rs4924575	0.96[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924576	0.92[CEU][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924580	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62002090	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62002091	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8025714	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8035855	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs890498	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs890505	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9672298	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9672360	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9920903	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv1036086	chr15:42004962-42091451	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1038894	chr15:42038152-42077452	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2757597	chr15:42047173-42122617	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2760027	chr15:42047173-42122617	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv904113	chr15:42050390-42118971	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv904114	chr15:42050390-42119900	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1918310	NDUFAF1	cis	parietal	SCAN
rs1918310	MAPKBP1	cis	cerebellum	SCAN
rs1918310	SPTBN5	cis	cerebellum	SCAN
rs1918310	RPAP1	cis	lymphoblastoid	seeQTL
rs1918310	RPAP1	cis	parietal	SCAN
rs1918310	MGA	cis	lesional skin	skin_eQTL
rs1918310	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs1918310	JMJD7-PLA2G4B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42025200-42065400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:42056400-42066000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:42057600-42066000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:42059000-42065600	Weak transcription	Fetal Brain Male	brain
5	chr15:42059400-42066000	Weak transcription	Colonic Mucosa	Colon
6	chr15:42059600-42065400	Weak transcription	Gastric	stomach
7	chr15:42059600-42065400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:42059600-42065600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:42059600-42065800	Weak transcription	Pancreas	Pancrea
10	chr15:42059600-42066000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:42059600-42066200	Weak transcription	Aorta	Aorta
12	chr15:42059600-42066200	Weak transcription	Lung	lung
13	chr15:42059600-42066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:42059800-42065400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:42059800-42065600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:42059800-42065600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:42059800-42065600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:42059800-42066000	Weak transcription	Esophagus	oesophagus
19	chr15:42059800-42066200	Weak transcription	Ovary	ovary
20	chr15:42060000-42065400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr15:42060000-42065400	Weak transcription	Small Intestine	intestine
22	chr15:42060400-42065800	Weak transcription	Brain Germinal Matrix	brain
23	chr15:42060600-42065400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:42062400-42065800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr15:42062400-42066000	Weak transcription	Left Ventricle	heart
26	chr15:42062800-42065400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:42064200-42065400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:42064400-42065400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:42064400-42065400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:42064800-42065400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:42064800-42065600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr15:42064800-42065600	Enhancers	Primary B cells from cord blood	blood
33	chr15:42064800-42065600	Enhancers	HSMM	muscle
34	chr15:42064800-42065800	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr15:42064800-42065800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:42064800-42065800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:42064800-42065800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr15:42064800-42065800	Enhancers	HMEC	breast
39	chr15:42064800-42066000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:42064800-42066000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr15:42065000-42065400	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr15:42065000-42065400	Enhancers	NHLF	lung
43	chr15:42065000-42065600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:42065000-42065600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:42065000-42065600	Enhancers	K562	blood
46	chr15:42065000-42065800	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr15:42065000-42065800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr15:42065000-42065800	Enhancers	Fetal Stomach	stomach
49	chr15:42065000-42066000	Enhancers	Primary B cells from peripheral blood	blood
50	chr15:42065000-42066000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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