Variant report

Variant	rs12658664
Chromosome Location	chr5:178986987-178986988
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	MXI1	chr5:178985457-178987460	SK-N-SH	brain:	n/a	n/a
2	SIN3AK20	chr5:178986065-178987144	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr5:178985798-178987122	GM12878	blood:	n/a	n/a
4	CEBPB	chr5:178986395-178987118	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:178986257-178987131	Gliobla	brain:	n/a	n/a
6	ETS1	chr5:178986677-178987173	A549	lung:	n/a	n/a
7	CEBPB	chr5:178985889-178987010	A549	lung:	n/a	n/a
8	MYC	chr5:178986718-178987222	MCF-7	breast:	n/a	n/a
9	POLR2A	chr5:178986270-178987125	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr5:178986261-178987092	A549	lung:	n/a	n/a
11	SP1	chr5:178986183-178987120	A549	lung:	n/a	chr5:178986611-178986625 chr5:178986510-178986519 chr5:178986509-178986518 chr5:178986510-178986519 chr5:178986616-178986625 chr5:178986615-178986624 chr5:178986614-178986626 chr5:178986614-178986626
12	MAX	chr5:178985914-178987175	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr5:178986334-178987012	HepG2	liver:	n/a	n/a
14	REST	chr5:178986717-178987026	A549	lung:	n/a	n/a
15	ELF1	chr5:178986353-178987142	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:178986194-178987011	GM12892	blood:	n/a	n/a
17	SP4	chr5:178986008-178987045	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr5:178985969-178987012	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr5:178986166-178987190	H1-neurons	neurons:	n/a	n/a
20	MYC	chr5:178985923-178987048	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr5:178985826-178987315	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr5:178985741-178987115	PANC-1	pancreas:	n/a	n/a
23	SP1	chr5:178985918-178987320	HCT-116	colon:	n/a	chr5:178986611-178986625 chr5:178986510-178986519 chr5:178986509-178986518 chr5:178986510-178986519 chr5:178986616-178986625 chr5:178986615-178986624 chr5:178986614-178986626 chr5:178986614-178986626
24	POLR2A	chr5:178986199-178987194	HL-60	blood:	n/a	n/a
25	SIN3AK20	chr5:178986668-178987046	A549	lung:	n/a	n/a
26	CHD2	chr5:178985950-178986993	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr5:178986281-178987048	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:178986201-178987054	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:178985838-178987112	PANC-1	pancreas:	n/a	n/a
30	SIN3AK20	chr5:178986310-178986988	SK-N-SH	brain:	n/a	n/a
31	SIN3AK20	chr5:178986210-178987135	A549	lung:	n/a	n/a
32	PML	chr5:178985993-178987118	MCF-7	breast:	n/a	chr5:178986488-178986496
33	POLR2A	chr5:178985734-178987380	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr5:178986026-178987152	HepG2	liver:	n/a	n/a
35	TAF1	chr5:178985949-178987287	H1-hESC	embryonic stem cell:	n/a	n/a
36	NFIC	chr5:178986297-178987149	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr5:178986298-178987128	Hela-S3	cervix:	n/a	n/a
38	GABPA	chr5:178986095-178987067	MCF-7	breast:	n/a	n/a
39	MAX	chr5:178985900-178987269	ECC-1	luminal epithelium:	n/a	n/a
40	MAX	chr5:178985887-178987449	MCF-7	breast:	n/a	n/a
41	POLR2A	chr5:178986188-178987235	HepG2	liver:	n/a	n/a
42	MAX	chr5:178985938-178987205	MCF-7	breast:	n/a	n/a
43	POLR2A	chr5:178986057-178987263	HEK293	kidney:	n/a	n/a
44	TCF7L2	chr5:178986025-178987139	HCT-116	colon:	n/a	n/a
45	MXI1	chr5:178986025-178987074	H1-hESC	embryonic stem cell:	n/a	n/a
46	MXI1	chr5:178986051-178986990	GM12878	blood:	n/a	n/a
47	POLR2A	chr5:178986002-178987314	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr5:178986001-178987011	SK-N-SH	brain:	n/a	n/a
49	GABPA	chr5:178986334-178987312	MCF-7	breast:	n/a	n/a
50	POLR2A	chr5:178985492-178987032	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:178986726..178988892-chr5:179104044..179106638,2	K562	blood:
2	chr5:178986094..178988194-chr5:179049451..179052935,4	MCF-7	breast:
3	chr5:178985235..178987908-chr5:179124412..179127341,2	MCF-7	breast:
4	chr5:178984205..178987569-chr5:178988108..178992792,6	MCF-7	breast:
5	chr5:178984558..178987542-chr5:178988263..178990973,3	K562	blood:
6	chr5:178986818..178988892-chr5:179105129..179106638,2	K562	blood:
7	chr5:178985192..178988541-chr5:179048594..179052191,5	MCF-7	breast:

Variant related genes	Relation type
RUFY1	TF binding region
ENSG00000176783	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000169045	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10064596	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10074573	0.91[MEX][hapmap]
rs10078712	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10078796	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10479542	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12652495	0.82[EUR][1000 genomes]
rs13179470	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4131080	0.85[CEU][hapmap];0.80[GIH][hapmap];0.83[TSI][hapmap]
rs4376229	0.80[CEU][hapmap];0.80[GIH][hapmap]
rs4701130	0.82[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4701131	0.86[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4701132	1.00[CEU][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6601050	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6896940	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7702303	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7703730	1.00[CEU][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7704349	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718673	0.80[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7723230	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7736163	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv531996	chr5:178669297-178989687	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
6	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
7	nsv1022509	chr5:178950829-179002751	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv883269	chr5:178951106-179031595	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
10	nsv1015477	chr5:178954409-179016804	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv883271	chr5:178955046-179031595	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv883272	chr5:178961872-179031595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv1028236	chr5:178962087-179019981	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12658664	RUFY1	cis	cerebellum	SCAN
rs12658664	C5orf45	cis	cerebellum	SCAN
rs12658664	RUFY1	cis	parietal	SCAN
rs12658664	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178981200-178996200	Weak transcription	K562	blood
2	chr5:178985600-178987000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:178985600-178987000	Active TSS	Brain Germinal Matrix	brain
4	chr5:178985600-178987000	Active TSS	HSMM	muscle
5	chr5:178985600-178987200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:178985600-178987400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr5:178985600-178987400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:178985600-178987600	Active TSS	A549	lung
9	chr5:178985800-178987000	Active TSS	H1 Cell Line	embryonic stem cell
10	chr5:178985800-178987000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:178985800-178987000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:178985800-178987000	Active TSS	Brain Cingulate Gyrus	brain
13	chr5:178985800-178987000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr5:178985800-178987000	Active TSS	Brain Substantia Nigra	brain
15	chr5:178985800-178987000	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr5:178985800-178987000	Active TSS	Fetal Lung	lung
17	chr5:178985800-178987000	Active TSS	Fetal Stomach	stomach
18	chr5:178985800-178987000	Active TSS	Right Atrium	heart
19	chr5:178985800-178987000	Active TSS	GM12878-XiMat	blood
20	chr5:178985800-178987000	Active TSS	NHDF-Ad	bronchial
21	chr5:178985800-178987000	Active TSS	NHLF	lung
22	chr5:178985800-178987200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr5:178985800-178987200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:178985800-178987200	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr5:178985800-178987200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:178985800-178987200	Active TSS	Fetal Intestine Large	intestine
27	chr5:178985800-178987400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr5:178985800-178987400	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr5:178985800-178987400	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr5:178985800-178987400	Active TSS	Fetal Kidney	kidney
31	chr5:178985800-178987400	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr5:178985800-178987400	Active TSS	HepG2	liver
33	chr5:178985800-178987600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:178986000-178987000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr5:178986000-178987000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr5:178986000-178987000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:178986000-178987000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr5:178986000-178987000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:178986000-178987000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:178986000-178987000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:178986000-178987000	Active TSS	Brain Anterior Caudate	brain
42	chr5:178986000-178987000	Active TSS	Brain Hippocampus Middle	brain
43	chr5:178986000-178987000	Active TSS	Fetal Brain Female	brain
44	chr5:178986000-178987000	Active TSS	Fetal Intestine Small	intestine
45	chr5:178986000-178987000	Active TSS	Stomach Mucosa	stomach
46	chr5:178986000-178987200	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr5:178986000-178987200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr5:178986000-178987200	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr5:178986000-178987200	Active TSS	Aorta	Aorta
50	chr5:178986000-178987200	Active TSS	Ovary	ovary

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