Variant report

Variant	rs11948056
Chromosome Location	chr5:90680468-90680469
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	POLR2A	chr5:90674657-90680962	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr5:90680351-90681015	GM12878	blood:	n/a	chr5:90680568-90680577
3	FOS	chr5:90680290-90680794	HUVEC	blood vessel:	n/a	chr5:90680565-90680576 chr5:90680569-90680578 chr5:90680567-90680578
4	FOS	chr5:90679910-90680997	MCF10A-Er-Src	breast:	n/a	chr5:90680565-90680576 chr5:90680569-90680578 chr5:90680567-90680578
5	GATA1	chr5:90675347-90681151	PBDE	blood:	n/a	chr5:90680794-90680801 chr5:90680794-90680803 chr5:90680794-90680801 chr5:90675376-90675387 chr5:90680567-90680576 chr5:90680794-90680801
6	REST	chr5:90680384-90681074	A549	lung:	n/a	n/a
7	REST	chr5:90670312-90680754	H1-neurons	neurons:	n/a	chr5:90679211-90679220 chr5:90679214-90679227 chr5:90676125-90676138 chr5:90676125-90676138
8	ARID3A	chr5:90680236-90681148	HepG2	liver:	n/a	n/a
9	FOS	chr5:90680385-90680998	MCF10A-Er-Src	breast:	n/a	chr5:90680565-90680576 chr5:90680569-90680578 chr5:90680567-90680578
10	JUND	chr5:90680351-90681036	K562	blood:	n/a	chr5:90680565-90680576 chr5:90680569-90680578
11	POLR2A	chr5:90678204-90681091	PANC-1	pancreas:	n/a	n/a
12	IRF1	chr5:90678324-90681092	K562	blood:	n/a	chr5:90678566-90678576 chr5:90680223-90680240 chr5:90678566-90678580 chr5:90678565-90678577 chr5:90680301-90680311 chr5:90680568-90680577
13	POLR2A	chr5:90674512-90681010	IMR90	lung:	n/a	n/a
14	SMC3	chr5:90678305-90681090	Hela-S3	cervix:	n/a	chr5:90680818-90680832 chr5:90680896-90680910
15	POU2F2	chr5:90680457-90681007	GM12878	blood:	n/a	chr5:90680766-90680777 chr5:90680765-90680775 chr5:90680764-90680776 chr5:90680694-90680708 chr5:90680763-90680778 chr5:90680768-90680781 chr5:90680766-90680776 chr5:90680692-90680706 chr5:90680768-90680781 chr5:90680695-90680706 chr5:90680760-90680782 chr5:90680690-90680712 chr5:90680762-90680775 chr5:90680691-90680704 chr5:90680766-90680775 chr5:90680761-90680782 chr5:90680691-90680704 chr5:90680765-90680775 chr5:90680768-90680781 chr5:90680691-90680704 chr5:90680762-90680780 chr5:90680767-90680774 chr5:90680767-90680775 chr5:90680766-90680777
16	NFYA	chr5:90680433-90681008	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:90662204-90681025	K562	blood:	n/a	n/a
18	CHD1	chr5:90675198-90681229	IMR90	lung:	n/a	chr5:90676000-90676010 chr5:90676134-90676144
19	CTCF	chr5:90678162-90681524	A549	lung:	n/a	chr5:90680895-90680911 chr5:90680811-90680832 chr5:90680816-90680834 chr5:90680894-90680912 chr5:90680822-90680831 chr5:90680901-90680908 chr5:90680889-90680910
20	RAD21	chr5:90680185-90681101	IMR90	lung:	n/a	chr5:90680823-90680832 chr5:90680814-90680833 chr5:90680901-90680910 chr5:90680892-90680911
21	MAFK	chr5:90680451-90681012	IMR90	lung:	n/a	n/a
22	POLR2A	chr5:90674350-90681014	H1-neurons	neurons:	n/a	n/a
23	RFX5	chr5:90674386-90681110	SK-N-SH	brain:	n/a	chr5:90675231-90675240 chr5:90676876-90676890 chr5:90676875-90676890 chr5:90676872-90676889 chr5:90676937-90676953 chr5:90676873-90676888 chr5:90676878-90676887 chr5:90675229-90675243 chr5:90677081-90677089 chr5:90676856-90676865
24	JUND	chr5:90680412-90681053	Hela-S3	cervix:	n/a	chr5:90680565-90680576 chr5:90680569-90680578
25	TBP	chr5:90674552-90681057	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr5:90680456-90681169	A549	lung:	n/a	chr5:90680823-90680832 chr5:90680814-90680833 chr5:90680901-90680910 chr5:90680892-90680911
27	RAD21	chr5:90680348-90681243	A549	lung:	n/a	chr5:90680823-90680832 chr5:90680814-90680833 chr5:90680901-90680910 chr5:90680892-90680911
28	RFX5	chr5:90680414-90681068	Hela-S3	cervix:	n/a	n/a
29	CHD1	chr5:90674406-90680925	H1-hESC	embryonic stem cell:	n/a	chr5:90676000-90676010 chr5:90676134-90676144
30	POLR2A	chr5:90672283-90680674	U87	brain:	n/a	n/a
31	SMC3	chr5:90678805-90681118	SK-N-SH	brain:	n/a	chr5:90680818-90680832 chr5:90680896-90680910
32	ARID3A	chr5:90679882-90681129	K562	blood:	n/a	n/a
33	CEBPB	chr5:90680303-90681005	Hela-S3	cervix:	n/a	chr5:90680321-90680333
34	RCOR1	chr5:90680391-90680990	K562	blood:	n/a	n/a
35	POLR2A	chr5:90675657-90680579	Raji	blood:	n/a	n/a
36	POLR2A	chr5:90680404-90681015	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr5:90674399-90680968	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr5:90675560-90680516	GM12878	blood:	n/a	n/a
39	ZC3H11A	chr5:90678978-90681007	K562	blood:	n/a	n/a
40	POLR2A	chr5:90661633-90680586	U87	brain:	n/a	n/a
41	POLR2A	chr5:90680439-90680610	HUVEC	blood vessel:	n/a	n/a
42	RAD21	chr5:90680415-90681136	Hela-S3	cervix:	n/a	chr5:90680823-90680832 chr5:90680814-90680833 chr5:90680901-90680910 chr5:90680892-90680911
43	CTCF	chr5:90680445-90681140	GM12878	blood:	n/a	chr5:90680894-90680912 chr5:90680811-90680832 chr5:90680816-90680834 chr5:90680901-90680908 chr5:90680895-90680911 chr5:90680889-90680910 chr5:90680822-90680831
44	STAT3	chr5:90680341-90681024	MCF10A-Er-Src	breast:	n/a	chr5:90680921-90680935
45	RAD21	chr5:90680357-90681248	HCT-116	colon:	n/a	chr5:90680823-90680832 chr5:90680814-90680833 chr5:90680901-90680910 chr5:90680892-90680911
46	MXI1	chr5:90675125-90681158	SK-N-SH	brain:	n/a	chr5:90676872-90676887 chr5:90677625-90677634
47	POLR2A	chr5:90672283-90681023	U87	brain:	n/a	n/a
48	POLR2A	chr5:90672032-90680664	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr5:90661706-90680586	U87	brain:	n/a	n/a
50	CTCF	chr5:90679769-90681306	SK-N-SH	brain:	n/a	chr5:90680894-90680912 chr5:90680811-90680832 chr5:90680816-90680834 chr5:90680901-90680908 chr5:90680895-90680911 chr5:90680889-90680910 chr5:90680822-90680831

No.	Distal block	Cell Line	Cell type
1	chr5:90573090..90582351-chr5:90673821..90680716,23	K562	blood:
2	chr5:90574103..90582351-chr5:90673173..90681609,28	K562	blood:
3	chr5:90605667..90612137-chr5:90676262..90681561,13	K562	blood:
4	chr5:90227664..90228224-chr5:90680158..90680912,2	K562	blood:
5	chr5:90397349..90398324-chr5:90680411..90681271,7	MCF-7	breast:
6	chr5:90680462..90681382-chr5:90715128..90715985,2	K562	blood:
7	chr5:90541796..90542359-chr5:90680035..90680971,3	K562	blood:
8	chr5:90161808..90162821-chr5:90680412..90681352,6	K562	blood:
9	chr5:90160809..90161588-chr5:90680384..90681060,3	MCF-7	breast:
10	chr5:90184781..90186579-chr5:90679255..90681231,2	MCF-7	breast:
11	chr5:90574805..90578594-chr5:90673900..90681432,13	MCF-7	breast:
12	chr5:90512455..90524285-chr5:90673793..90683360,52	MCF-7	breast:
13	chr5:89704232..89708009-chr5:90677895..90680741,3	K562	blood:
14	chr5:90607284..90611861-chr5:90674569..90683045,11	K562	blood:
15	chr5:90521677..90522591-chr5:90680450..90681318,6	MCF-7	breast:
16	chr5:90560937..90569122-chr5:90675177..90680484,12	K562	blood:
17	chr5:90521115..90522384-chr5:90680284..90681436,9	K562	blood:
18	chr5:90520446..90522907-chr5:90680193..90681317,25	MCF-7	breast:
19	chr5:90607483..90611926-chr5:90672625..90681906,20	MCF-7	breast:
20	chr5:90397347..90398313-chr5:90679537..90681364,7	K562	blood:
21	chr5:90099269..90102186-chr5:90679396..90681079,2	MCF-7	breast:
22	chr5:90227784..90228309-chr5:90680384..90681178,2	MCF-7	breast:
23	chr5:90512732..90524610-chr5:90674652..90682171,24	K562	blood:
24	chr5:90513015..90523645-chr5:90674785..90682171,21	K562	blood:
25	chr5:90515350..90516235-chr5:90680436..90681312,5	MCF-7	breast:
26	chr5:90510244..90526030-chr5:90672528..90682389,53	MCF-7	breast:

Variant related genes	Relation type
ARRDC3	TF binding region
ENSG00000255647	Chromatin interaction
ENSG00000248323	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000271762	Chromatin interaction
ENSG00000212930	Chromatin interaction
ENSG00000199643	Chromatin interaction
ENSG00000251093	Chromatin interaction
ENSG00000234292	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10041402	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10045280	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10052492	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10054820	0.87[EUR][1000 genomes]
rs10058025	0.90[EUR][1000 genomes]
rs10059163	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10063683	0.90[EUR][1000 genomes]
rs10073657	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10073935	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1035476	0.86[EUR][1000 genomes]
rs1035477	0.87[EUR][1000 genomes]
rs10474352	0.88[EUR][1000 genomes]
rs10474353	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10942634	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11948075	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11950530	0.90[EUR][1000 genomes]
rs11955120	0.86[EUR][1000 genomes]
rs11959525	0.90[EUR][1000 genomes]
rs12110065	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12110303	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12188467	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12651840	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12654787	0.90[EUR][1000 genomes]
rs12655973	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12656350	0.87[EUR][1000 genomes]
rs1363839	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1477348	0.90[EUR][1000 genomes]
rs1477349	0.90[EUR][1000 genomes]
rs186717	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1895448	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1895449	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1964292	0.85[EUR][1000 genomes]
rs1966494	0.87[EUR][1000 genomes]
rs2004483	0.88[EUR][1000 genomes]
rs2052553	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2059207	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2059208	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2367353	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2367526	0.85[EUR][1000 genomes]
rs2839728	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2887007	0.85[EUR][1000 genomes]
rs332544	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35712350	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4382199	0.87[EUR][1000 genomes]
rs60513756	0.88[EUR][1000 genomes]
rs6452951	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6452953	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6452954	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66759971	0.86[EUR][1000 genomes]
rs6860948	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6865495	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6866191	0.87[EUR][1000 genomes]
rs6866923	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6867091	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6869048	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6869717	0.90[EUR][1000 genomes]
rs6882269	0.90[EUR][1000 genomes]
rs746637	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7705465	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7708782	0.88[EUR][1000 genomes]
rs7715402	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7718871	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7720132	0.86[EUR][1000 genomes]
rs7720235	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs889213	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9293568	0.87[EUR][1000 genomes]
rs9686361	0.87[EUR][1000 genomes]
rs985434	0.87[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	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90673800-90680800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:90674000-90680800	Active TSS	K562	blood
3	chr5:90674400-90680800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:90674600-90680600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:90674600-90680600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:90674600-90680600	Active TSS	Psoas Muscle	Psoas
7	chr5:90674600-90680600	Active TSS	Right Ventricle	heart
8	chr5:90674600-90680800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:90674800-90680800	Active TSS	Stomach Mucosa	stomach
10	chr5:90675000-90680600	Active TSS	Fetal Intestine Large	intestine
11	chr5:90675000-90680800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr5:90675000-90680800	Active TSS	NHEK	skin
13	chr5:90675000-90681000	Active TSS	Thymus	Thymus
14	chr5:90675200-90680600	Active TSS	Placenta	Placenta
15	chr5:90675400-90680800	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr5:90675400-90680800	Active TSS	Colonic Mucosa	Colon
17	chr5:90677400-90680800	Active TSS	Fetal Brain Female	brain
18	chr5:90677400-90681000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:90678400-90680800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:90679400-90680600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr5:90679400-90680800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr5:90679400-90680800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr5:90679400-90680800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:90679400-90680800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:90679400-90680800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr5:90679600-90680600	Flanking Active TSS	Fetal Thymus	thymus
27	chr5:90679600-90680600	Active TSS	Right Atrium	heart
28	chr5:90679600-90680800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr5:90679600-90680800	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr5:90679600-90680800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:90679600-90680800	Flanking Active TSS	HUVEC	blood vessel
32	chr5:90679800-90680600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:90679800-90680600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr5:90679800-90680600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr5:90679800-90680600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr5:90679800-90680600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:90679800-90680600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr5:90679800-90680600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr5:90679800-90680600	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr5:90679800-90680800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:90679800-90680800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr5:90679800-90680800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr5:90679800-90680800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr5:90679800-90680800	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr5:90679800-90680800	Flanking Active TSS	Fetal Brain Male	brain
46	chr5:90679800-90680800	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr5:90679800-90680800	Flanking Active TSS	Dnd41	blood
48	chr5:90679800-90680800	Flanking Active TSS	Hela-S3	cervix
49	chr5:90679800-90680800	Flanking Active TSS	NH-A	brain
50	chr5:90680000-90680600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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