Variant report

Variant	rs334930
Chromosome Location	chr15:76350112-76350113
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	RELA	chr15:76349212-76350120	GM12891	blood:	n/a	n/a
2	RAD21	chr15:76349795-76350151	HepG2	liver:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
3	RAD21	chr15:76349685-76350166	ECC-1	luminal epithelium:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
4	RAD21	chr15:76349735-76350179	A549	lung:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
5	CTCF	chr15:76349431-76350151	GM12878	blood:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349476-76349484 chr15:76349960-76349981 chr15:76349958-76349976
6	RAD21	chr15:76349725-76350132	MCF-7	breast:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
7	RAD21	chr15:76349747-76350128	IMR90	lung:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
8	SMC3	chr15:76349781-76350137	K562	blood:	n/a	chr15:76349964-76349974 chr15:76349960-76349974
9	MYC	chr15:76349423-76350195	MCF10A-Er-Src	breast:	n/a	chr15:76349525-76349535
10	CTCF	chr15:76349731-76350115	MCF-7	breast:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
11	CTCF	chr15:76349182-76352137	A549	lung:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349476-76349484 chr15:76349960-76349981 chr15:76349958-76349976
12	SMC3	chr15:76349230-76350153	GM12878	blood:	n/a	chr15:76349964-76349974 chr15:76349960-76349974
13	RAD21	chr15:76349680-76350166	A549	lung:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
14	CTCF	chr15:76349756-76350349	K562	blood:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
15	CTCF	chr15:76349518-76350887	SK-N-SH	brain:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
16	RAD21	chr15:76349785-76350149	H1-hESC	embryonic stem cell:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
17	RAD21	chr15:76349679-76350249	HepG2	liver:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
18	RAD21	chr15:76349754-76350164	ECC-1	luminal epithelium:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
19	ZNF143	chr15:76349208-76350134	GM12878	blood:	n/a	n/a
20	CTCF	chr15:76349720-76350154	MCF-7	breast:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
21	CTCF	chr15:76349740-76350164	HepG2	liver:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
22	ZNF143	chr15:76349783-76350122	H1-hESC	embryonic stem cell:	n/a	n/a
23	RAD21	chr15:76349741-76350150	H1-hESC	embryonic stem cell:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
24	YY1	chr15:76349803-76350128	GM12878	blood:	n/a	n/a
25	SMC3	chr15:76349771-76350145	HepG2	liver:	n/a	chr15:76349964-76349974 chr15:76349960-76349974
26	RAD21	chr15:76349242-76350353	SK-N-SH	brain:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
27	CTCF	chr15:76349627-76350133	A549	lung:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
28	SMC3	chr15:76349584-76350151	SK-N-SH	brain:	n/a	chr15:76349964-76349974 chr15:76349960-76349974
29	MXI1	chr15:76349688-76350152	SK-N-SH	brain:	n/a	n/a
30	RAD21	chr15:76349544-76350151	GM12878	blood:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
31	RAD21	chr15:76349701-76350147	HCT-116	colon:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
32	CTCF	chr15:76349671-76350176	HCT-116	colon:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
33	CTCF	chr15:76349746-76350114	H1-hESC	embryonic stem cell:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
34	CTCF	chr15:76349980-76350130	HFF-Myc	foreskin:	n/a	n/a
35	CTCF	chr15:76349745-76350155	IMR90	lung:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
36	CTCF	chr15:76349589-76350287	HCT-116	colon:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
37	SMC3	chr15:76349615-76350153	Hela-S3	cervix:	n/a	chr15:76349964-76349974 chr15:76349960-76349974
38	RAD21	chr15:76349662-76350298	HCT-116	colon:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
39	RAD21	chr15:76349437-76350149	Hela-S3	cervix:	n/a	chr15:76349964-76349974 chr15:76349964-76349976 chr15:76349959-76349978 chr15:76349962-76349975
40	CTCF	chr15:76349739-76350140	K562	blood:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976
41	RELA	chr15:76349145-76350128	GM12878	blood:	n/a	n/a
42	RFX5	chr15:76349794-76350121	Hela-S3	cervix:	n/a	n/a
43	FOS	chr15:76349221-76350116	MCF10A-Er-Src	breast:	n/a	chr15:76349662-76349669 chr15:76349366-76349375 chr15:76349662-76349671
44	CTCF	chr15:76349734-76350180	K562	blood:	n/a	chr15:76349961-76349974 chr15:76349963-76349973 chr15:76349960-76349981 chr15:76349958-76349976

No.	Distal block	Cell Line	Cell type
1	chr15:76349917..76350459-chr15:76440383..76440942,2	K562	blood:
2	chr15:76195094..76197177-chr15:76350015..76352498,2	K562	blood:
3	chr15:76341281..76343239-chr15:76349906..76351616,2	MCF-7	breast:
4	chr15:76349862..76350383-chr15:76442992..76443858,2	MCF-7	breast:

Variant related genes	Relation type
C15orf27	TF binding region
NRG4	TF binding region
ENSG00000167196	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12910576	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12915012	0.81[AMR][1000 genomes]
rs1391894	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1699263	0.92[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs184580	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs189197	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2255701	1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs2455899	0.93[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap]
rs2460798	0.93[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap]
rs2469039	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2593280	0.93[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap]
rs28876229	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2955733	1.00[GIH][hapmap];0.84[LWK][hapmap]
rs2955746	0.85[YRI][hapmap]
rs2959842	1.00[GIH][hapmap]
rs2959852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334934	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334936	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs335681	0.93[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs335697	1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs335706	0.91[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs335711	1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs4886747	0.81[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.96[TSI][hapmap]
rs4886753	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4886754	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71403522	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8024155	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs985849	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904398	chr15:76220285-76359055	Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1617	chr15:76332103-76359435	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1048760	chr15:76334544-76496977	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs334930	NRG4	cis	frontal cortex	BrainEAC
rs334930	NRG4	cis	temporal cortex	BrainEAC
rs334930	NRG4	cis	brain	BrainEAC
rs334930	NRG4	cis	substantia nigra	BrainEAC
rs334930	NRG4	cis	intralobular white matter	BrainEAC
rs334930	NRG4	cis	putamen	BrainEAC
rs334930	NRG4	cis	occipital cortex	BrainEAC
rs334930	NRG4	cis	cerebellar cortex	BrainEAC
rs334930	NRG4	cis	thalamus	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76349400-76351000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:76349600-76350800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:76349600-76351400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:76349800-76350200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr15:76349800-76351000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:76349800-76351200	Active TSS	Brain Angular Gyrus	brain
7	chr15:76350000-76350200	Enhancers	Brain Anterior Caudate	brain
8	chr15:76350000-76350400	Enhancers	Primary hematopoietic stem cells	blood
9	chr15:76350000-76350400	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:76350000-76350400	Enhancers	GM12878-XiMat	blood
11	chr15:76350000-76350800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:76350000-76350800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:76350000-76351200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:76350000-76351200	Weak transcription	Pancreas	Pancrea
15	chr15:76350000-76351200	Weak transcription	Psoas Muscle	Psoas
16	chr15:76350000-76351200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:76350000-76351200	Enhancers	HMEC	breast
18	chr15:76350000-76351400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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