Variant report

Variant	rs4563584
Chromosome Location	chr5:179049329-179049330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:59)
CpG islands
(count:0)
Chromatin interactive
region (count:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:59 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179047206-179051952	GM12878	blood:	n/a	n/a
2	GATA3	chr5:179048795-179049367	SH-SY5Y	brain:	n/a	chr5:179049190-179049198
3	POLR2A	chr5:179049295-179051786	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA1	chr5:179047367-179049842	PBDE	blood:	n/a	chr5:179049745-179049762
5	CHD1	chr5:179047686-179052125	IMR90	lung:	n/a	chr5:179050801-179050811 chr5:179051151-179051161
6	POLR2A	chr5:179046881-179049431	K562	blood:	n/a	n/a
7	POLR2A	chr5:179046685-179051229	HepG2	liver:	n/a	n/a
8	POLR2A	chr5:179046804-179051909	U87	brain:	n/a	n/a
9	MXI1	chr5:179049238-179051776	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:179046855-179052674	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:179047240-179052213	SK-N-MC	brain:	n/a	n/a
12	SIN3AK20	chr5:179049279-179051150	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr5:179047285-179051399	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr5:179047201-179051828	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:179049224-179052039	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr5:179039431-179049902	HepG2	liver:	n/a	n/a
17	POLR2A	chr5:179047240-179049937	GM12892	blood:	n/a	n/a
18	POLR2A	chr5:179047237-179052054	GM12892	blood:	n/a	n/a
19	POLR2A	chr5:179047230-179049921	GM12891	blood:	n/a	n/a
20	HEY1	chr5:179048562-179049498	HepG2	liver:	n/a	n/a
21	POLR2A	chr5:179046790-179052167	PANC-1	pancreas:	n/a	n/a
22	TAL1	chr5:179047469-179051205	K562	blood:	n/a	n/a
23	CEBPB	chr5:179049205-179050121	A549	lung:	n/a	chr5:179049837-179049848 chr5:179049839-179049848 chr5:179049326-179049337 chr5:179049839-179049848 chr5:179049324-179049337 chr5:179049839-179049848
24	CHD1	chr5:179048407-179051414	H1-hESC	embryonic stem cell:	n/a	chr5:179050801-179050811 chr5:179051151-179051161
25	POLR2A	chr5:179047292-179049924	GM12892	blood:	n/a	n/a
26	POLR2A	chr5:179046078-179049406	GM12878	blood:	n/a	n/a
27	POLR2A	chr5:179046731-179051978	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr5:179049079-179049415	GM12891	blood:	n/a	n/a
29	POLR2A	chr5:179049211-179049938	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr5:179046899-179052266	H1-hESC	embryonic stem cell:	n/a	n/a
31	MXI1	chr5:179047845-179049445	K562	blood:	n/a	n/a
32	GATA2	chr5:179048653-179049451	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr5:179049155-179049931	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr5:179047285-179051765	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr5:179049138-179049933	GM12891	blood:	n/a	n/a
36	POLR2A	chr5:179049136-179051972	GM12892	blood:	n/a	n/a
37	POLR2A	chr5:179049277-179051946	K562	blood:	n/a	n/a
38	POLR2A	chr5:179043848-179051855	MCF-7	breast:	n/a	n/a
39	POLR2A	chr5:179046694-179049912	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr5:179047671-179052143	K562	blood:	n/a	n/a
41	CEBPB	chr5:179049177-179050069	Hela-S3	cervix:	n/a	chr5:179049837-179049848 chr5:179049839-179049848 chr5:179049326-179049337 chr5:179049839-179049848 chr5:179049324-179049337 chr5:179049839-179049848
42	POLR2A	chr5:179047255-179052025	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr5:179046884-179052061	GM12891	blood:	n/a	n/a
44	KAP1	chr5:179048200-179049350	K562	blood:	n/a	n/a
45	POLR2A	chr5:179046931-179052092	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr5:179046889-179051904	GM12878	blood:	n/a	n/a
47	POLR2A	chr5:179046832-179051357	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr5:179049307-179052118	K562	blood:	n/a	n/a
49	HEY1	chr5:179047688-179049932	K562	blood:	n/a	n/a
50	POLR2A	chr5:179046804-179051915	U87	brain:	n/a	n/a

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179049295..179049929-chr5:179095089..179095660,2	K562	blood:
2	chr5:179049028..179050758-chr5:179230503..179232044,2	K562	blood:
3	chr15:69753495..69755844-chr5:179048677..179051620,2	MCF-7	breast:
4	chr5:179048674..179050755-chr5:179131427..179133888,2	MCF-7	breast:
5	chr5:178993088..178996882-chr5:179048174..179052059,4	K562	blood:
6	chr5:179047581..179051358-chr5:179102429..179108878,16	K562	blood:
7	chr5:179048487..179050192-chr5:179084037..179087067,3	K562	blood:
8	chr5:179049088..179052063-chr5:179245796..179250145,6	MCF-7	breast:
9	chr5:179003044..179005228-chr5:179048934..179051877,3	K562	blood:
10	chr5:179047278..179052613-chr5:179246048..179251997,13	K562	blood:
11	chr5:178985192..178988541-chr5:179048594..179052191,5	MCF-7	breast:
12	chr5:179013908..179017053-chr5:179048415..179051520,3	K562	blood:
13	chr5:178882272..178884920-chr5:179049238..179052060,2	K562	blood:
14	chr5:179047959..179050192-chr5:179084037..179087067,3	K562	blood:
15	chr5:179049042..179051273-chr5:179225764..179228331,2	MCF-7	breast:
16	chr5:179047637..179052326-chr5:179245599..179249536,7	K562	blood:
17	chr5:179047831..179051506-chr5:179245810..179250436,9	MCF-7	breast:
18	chr5:179023314..179026919-chr5:179048927..179051890,4	MCF-7	breast:
19	chr5:179049208..179051645-chr5:179125705..179129690,6	MCF-7	breast:
20	chr5:179048811..179053260-chr5:179101652..179108160,8	MCF-7	breast:
21	chr5:179049178..179050682-chr5:179227339..179229062,2	MCF-7	breast:
22	chr5:178975871..178983601-chr5:179047224..179052413,15	K562	blood:
23	chr5:179048743..179051829-chr5:179229515..179233744,4	MCF-7	breast:
24	chr5:178989508..178991362-chr5:179048413..179051335,2	MCF-7	breast:
25	chr5:179048156..179052144-chr5:179103013..179109071,12	K562	blood:
26	chr5:178975440..178984076-chr5:179047224..179053131,17	K562	blood:
27	chr5:179048548..179052839-chr5:179221765..179224480,6	MCF-7	breast:
28	chr5:179049048..179052854-chr5:179122221..179127718,16	MCF-7	breast:
29	chr5:178976539..178978410-chr5:179046983..179049342,2	MCF-7	breast:
30	chr5:179047558..179053114-chr5:179123905..179129187,22	K562	blood:
31	chr5:179049195..179052432-chr5:179232038..179235083,3	K562	blood:
32	chr5:179049252..179051807-chr5:179078099..179079783,3	MCF-7	breast:
33	chr5:179048168..179052824-chr5:179156969..179161337,9	MCF-7	breast:
34	chr2:61403577..61406142-chr5:179049162..179051575,2	MCF-7	breast:
35	chr5:179045239..179052804-chr5:179123707..179130726,40	K562	blood:

No data

Variant related genes	Relation type
HNRNPH1	TF binding region
ENSG00000161021	Chromatin interaction
ENSG00000250999	Chromatin interaction
ENSG00000250674	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000204659	Chromatin interaction
ENSG00000245750	Chromatin interaction
ENSG00000173209	Chromatin interaction
ENSG00000228259	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000259215	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10054335	0.91[ASN][1000 genomes]
rs10056863	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs11249649	0.86[ASN][1000 genomes]
rs1136267	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs12719865	0.89[JPT][hapmap]
rs4078141	0.83[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs4256313	0.91[ASN][1000 genomes]
rs4336318	0.89[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4608884	0.88[CHD][hapmap]
rs4701143	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.84[YRI][hapmap];0.91[ASN][1000 genomes]
rs66479467	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6895677	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs7448707	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs7706275	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs8087	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs8180434	0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv883273	chr5:179045142-179086833	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
6	nsv823357	chr5:179046318-179058193	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4563584	RUFY1	cis	cerebellum	SCAN
rs4563584	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs4563584	HNRNPH1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179044400-179049400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
2	chr5:179044400-179049800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:179044400-179050600	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr5:179044600-179049800	Transcr. at gene 5' and 3'	A549	lung
5	chr5:179044800-179049400	Transcr. at gene 5' and 3'	K562	blood
6	chr5:179044800-179049800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr5:179044800-179049800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:179045000-179051200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:179045200-179049400	Transcr. at gene 5' and 3'	HUVEC	blood vessel
10	chr5:179045600-179049400	Transcr. at gene 5' and 3'	Hela-S3	cervix
11	chr5:179045600-179049400	Transcr. at gene 5' and 3'	NH-A	brain
12	chr5:179045600-179049400	Transcr. at gene 5' and 3'	Osteobl	bone
13	chr5:179045600-179049800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:179045600-179049800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
15	chr5:179045600-179049800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:179045600-179049800	Transcr. at gene 5' and 3'	Fetal Lung	lung
17	chr5:179045600-179050200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
18	chr5:179045800-179049400	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
19	chr5:179045800-179049400	Transcr. at gene 5' and 3'	HMEC	breast
20	chr5:179045800-179049400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
21	chr5:179045800-179049600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
22	chr5:179045800-179049800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:179045800-179050400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
24	chr5:179046000-179049400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
25	chr5:179046000-179049400	Transcr. at gene 5' and 3'	HepG2	liver
26	chr5:179046000-179049400	Transcr. at gene 5' and 3'	HSMM	muscle
27	chr5:179046000-179049600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:179046000-179049800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:179046000-179049800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:179046000-179050200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:179046000-179051200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
32	chr5:179046200-179049400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
33	chr5:179046200-179049400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
34	chr5:179046200-179049400	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
35	chr5:179046200-179049400	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:179046200-179049600	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
37	chr5:179046200-179049600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:179046200-179049600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:179046200-179049600	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
40	chr5:179046200-179049800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:179046200-179049800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
42	chr5:179046200-179049800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
43	chr5:179046200-179050200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:179046400-179049800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
45	chr5:179046600-179049400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
46	chr5:179046800-179049800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
47	chr5:179047000-179049400	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
48	chr5:179047000-179049800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
49	chr5:179047000-179049800	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
50	chr5:179047000-179049800	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell

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