Variant report

Variant	rs7616815
Chromosome Location	chr3:48779715-48779716
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	MAFF	chr3:48779666-48780029	K562	blood:	n/a	n/a
2	JUN	chr3:48779567-48780022	K562	blood:	n/a	chr3:48779912-48779919
3	RCOR1	chr3:48779659-48780072	K562	blood:	n/a	n/a
4	ZNF384	chr3:48779673-48780413	K562	blood:	n/a	n/a
5	CEBPB	chr3:48779627-48779888	A549	lung:	n/a	chr3:48779748-48779761
6	USF1	chr3:48779561-48780028	K562	blood:	n/a	n/a
7	BHLHE40	chr3:48779664-48780098	K562	blood:	n/a	n/a
8	POLR2A	chr3:48779634-48780045	K562	blood:	n/a	n/a
9	TEAD4	chr3:48779558-48780062	K562	blood:	n/a	n/a
10	MAZ	chr3:48779688-48780012	K562	blood:	n/a	chr3:48779749-48779758
11	STAT5A	chr3:48779645-48780112	K562	blood:	n/a	n/a
12	MYC	chr3:48779638-48779993	K562	blood:	n/a	chr3:48779749-48779758
13	CEBPB	chr3:48779529-48779990	K562	blood:	n/a	chr3:48779748-48779761
14	TEAD4	chr3:48779565-48780068	K562	blood:	n/a	n/a
15	ATF3	chr3:48779630-48779931	K562	blood:	n/a	n/a
16	CEBPB	chr3:48779685-48779892	Hela-S3	cervix:	n/a	chr3:48779748-48779761
17	POLR2A	chr3:48779697-48780023	K562	blood:	n/a	n/a
18	MAX	chr3:48779642-48779995	K562	blood:	n/a	chr3:48779749-48779758
19	MYC	chr3:48779665-48780045	K562	blood:	n/a	chr3:48779749-48779758
20	CEBPD	chr3:48779647-48780073	K562	blood:	n/a	n/a
21	POLR2A	chr3:48779653-48780069	K562	blood:	n/a	n/a
22	CEBPD	chr3:48779661-48780145	K562	blood:	n/a	n/a
23	CBX3	chr3:48779651-48780019	K562	blood:	n/a	n/a
24	JUND	chr3:48779622-48780071	K562	blood:	n/a	chr3:48779912-48779919
25	NR2F2	chr3:48779526-48780140	K562	blood:	n/a	n/a
26	FOS	chr3:48779708-48779866	MCF10A-Er-Src	breast:	n/a	n/a
27	CEBPB	chr3:48779618-48779927	IMR90	lung:	n/a	chr3:48779748-48779761
28	TBL1XR1	chr3:48779630-48780009	K562	blood:	n/a	n/a
29	EP300	chr3:48779623-48780068	K562	blood:	n/a	n/a
30	MAX	chr3:48779651-48780101	K562	blood:	n/a	chr3:48779749-48779758
31	ATF1	chr3:48779668-48779977	K562	blood:	n/a	n/a
32	CBX3	chr3:48779586-48780061	K562	blood:	n/a	n/a
33	TBP	chr3:48779661-48780088	K562	blood:	n/a	n/a
34	CEBPB	chr3:48779570-48779959	K562	blood:	n/a	chr3:48779748-48779761
35	MAX	chr3:48779674-48779986	K562	blood:	n/a	chr3:48779749-48779758
36	USF1	chr3:48779660-48779909	K562	blood:	n/a	n/a
37	GATA1	chr3:48779475-48780196	K562	blood:	n/a	n/a
38	ZMIZ1	chr3:48779705-48780000	K562	blood:	n/a	n/a
39	ARID3A	chr3:48779668-48779965	K562	blood:	n/a	n/a
40	GATA2	chr3:48779664-48779990	K562	blood:	n/a	n/a
41	POLR2A	chr3:48779705-48780109	K562	blood:	n/a	n/a
42	MAFK	chr3:48779681-48780019	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48698968..48701587-chr3:48778820..48781194,2	K562	blood:
2	chr3:48777662..48781214-chr3:48954479..48957215,3	K562	blood:
3	chr3:48778919..48781292-chr3:49044225..49047223,2	K562	blood:
4	chr3:48777544..48781186-chr3:48954650..48958375,5	K562	blood:
5	chr3:48778330..48780434-chr3:48788133..48790019,2	K562	blood:

Variant related genes	Relation type
IP6K2	TF binding region
ENSG00000178252	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000114302	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000221883	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 36 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10780033	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs10865952	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11130176	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1134591	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs11705737	0.81[EUR][1000 genomes]
rs11705888	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11920534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11924597	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11928552	0.92[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs12493289	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12493578	0.92[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs12497850	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13064911	0.81[EUR][1000 genomes]
rs13076394	0.81[EUR][1000 genomes]
rs13078308	0.80[EUR][1000 genomes]
rs13092715	0.90[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs13315711	0.82[EUR][1000 genomes]
rs1352420	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28642807	0.85[EUR][1000 genomes]
rs3774628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4072859	0.81[EUR][1000 genomes]
rs4858798	0.92[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs4858828	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs4858831	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs4974079	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs4974080	0.81[EUR][1000 genomes]
rs4974082	0.82[EUR][1000 genomes]
rs4974085	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs4974087	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs6414613	0.80[EUR][1000 genomes]
rs6442130	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446196	0.82[EUR][1000 genomes]
rs6446198	0.80[EUR][1000 genomes]
rs6446205	0.81[EUR][1000 genomes]
rs6446252	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6446253	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6781790	0.81[EUR][1000 genomes]
rs6786665	0.81[EUR][1000 genomes]
rs6788650	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6791234	0.80[EUR][1000 genomes]
rs6791542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7373778	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7430501	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs7431710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7431857	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs7612459	0.81[EUR][1000 genomes]
rs7623023	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7627404	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7628719	0.82[EUR][1000 genomes]
rs7630742	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7636057	0.82[EUR][1000 genomes]
rs7639332	0.84[EUR][1000 genomes]
rs7643368	0.81[EUR][1000 genomes]
rs7647813	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs7649458	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.83[EUR][1000 genomes]
rs7653459	0.81[EUR][1000 genomes]
rs9311430	0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9311432	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9311433	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9311434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9637481	1.00[CEU][hapmap]
rs9681717	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9682444	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9754878	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9755490	1.00[CEU][hapmap];0.90[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9830636	0.82[EUR][1000 genomes]
rs9835307	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9840684	0.86[EUR][1000 genomes]
rs9850134	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs9867373	0.80[EUR][1000 genomes]
rs9876848	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9879971	0.86[EUR][1000 genomes]
rs9884022	1.00[CEU][hapmap];0.81[EUR][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	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3407876	chr3:48774454-48823998	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:36)

SNP	Gene	Cis/trans	Tissue	Source
rs7616815	TLR9	cis	parietal	SCAN
rs7616815	NCKIPSD	cis	parietal	SCAN
rs7616815	DALRD3	cis	cerebellum	SCAN
rs7616815	CCDC71	cis	cerebellum	SCAN
rs7616815	NCKIPSD	cis	cerebellum	SCAN
rs7616815	WDR6	cis	lymphoblastoid	seeQTL
rs7616815	WDR6	cis	Nerve Tibial	GTEx
rs7616815	P4HTM	cis	cerebellum	SCAN
rs7616815	NICN1	cis	Thyroid	GTEx
rs7616815	NCKIPSD	cis	Nerve Tibial	GTEx
rs7616815	WDR6	cis	Muscle Skeletal	GTEx
rs7616815	WDR6	cis	Heart Left Ventricle	GTEx
rs7616815	ARIH2	cis	Thyroid	GTEx
rs7616815	AMT	cis	cerebellum	SCAN
rs7616815	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs7616815	WDR6	cis	Esophagus Muscularis	GTEx
rs7616815	AMT	cis	Whole Blood	GTEx
rs7616815	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs7616815	AMT	cis	parietal	SCAN
rs7616815	WDR6	cis	Esophagus Mucosa	GTEx
rs7616815	P4HTM	cis	parietal	SCAN
rs7616815	WDR6	cis	parietal	SCAN
rs7616815	NCKIPSD	cis	Muscle Skeletal	GTEx
rs7616815	WDR6	cis	cerebellum	SCAN
rs7616815	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs7616815	WDR6	cis	Whole Blood	GTEx
rs7616815	AMT	cis	Artery Aorta	GTEx
rs7616815	AMT	cis	Thyroid	GTEx
rs7616815	WDR6	cis	lung	GTEx
rs7616815	PHF7	cis	parietal	SCAN
rs7616815	WDR6	cis	Artery Tibial	GTEx
rs7616815	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs7616815	NICN1-AS1	cis	Thyroid	GTEx
rs7616815	WDR6	cis	Adipose Subcutaneous	GTEx
rs7616815	DALRD3	cis	parietal	SCAN
rs7616815	CCDC36	cis	Artery Tibial	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48772800-48780200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:48775600-48780000	Enhancers	Placenta	Placenta
3	chr3:48776200-48783200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:48776200-48784800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:48777400-48782600	Weak transcription	Aorta	Aorta
6	chr3:48777600-48787800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:48777800-48782600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:48777800-48783000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:48777800-48783200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:48777800-48783400	Weak transcription	Primary B cells from cord blood	blood
11	chr3:48777800-48784000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:48777800-48784400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:48777800-48784800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:48777800-48784800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:48777800-48784800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:48777800-48785000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:48777800-48785400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:48777800-48785800	Weak transcription	Spleen	Spleen
19	chr3:48777800-48788000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:48777800-48788800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:48777800-48807400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:48778000-48780000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:48778000-48780000	Enhancers	Brain Anterior Caudate	brain
24	chr3:48778000-48781200	Enhancers	K562	blood
25	chr3:48778000-48783200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:48778000-48788000	Weak transcription	HUVEC	blood vessel
27	chr3:48778000-48788200	Weak transcription	NH-A	brain
28	chr3:48778000-48788400	Weak transcription	GM12878-XiMat	blood
29	chr3:48778000-48789000	Weak transcription	NHEK	skin
30	chr3:48778000-48807200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:48778200-48779800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr3:48778200-48779800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr3:48778200-48780000	Enhancers	Brain Hippocampus Middle	brain
34	chr3:48778200-48780400	Enhancers	Adipose Nuclei	Adipose
35	chr3:48778200-48782600	Weak transcription	Fetal Intestine Small	intestine
36	chr3:48778200-48782800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:48778200-48782800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:48778200-48783000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:48778200-48783000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:48778200-48783000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:48778200-48783000	Weak transcription	Lung	lung
42	chr3:48778200-48783200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:48778200-48783200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:48778200-48783200	Weak transcription	HSMM	muscle
45	chr3:48778200-48783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:48778200-48783400	Weak transcription	Psoas Muscle	Psoas
47	chr3:48778200-48783800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:48778200-48784400	Weak transcription	Osteobl	bone
49	chr3:48778200-48784600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:48778200-48784600	Weak transcription	HMEC	breast

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