Variant report

Variant	rs59663860
Chromosome Location	chr11:47276350-47276351
allele	C/G
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	REST	chr11:47276256-47276811	PFSK-1	brain:	n/a	n/a
2	CTCF	chr11:47276340-47276490	GM12878	blood:	n/a	n/a
3	YY1	chr11:47276340-47276793	HepG2	liver:	n/a	n/a
4	EP300	chr11:47276298-47276743	HepG2	liver:	n/a	n/a
5	HNF4A	chr11:47276273-47277066	HepG2	liver:	n/a	chr11:47276954-47276966 chr11:47276960-47276975 chr11:47276954-47276967 chr11:47276953-47276968 chr11:47276953-47276968 chr11:47276960-47276975 chr11:47276953-47276967 chr11:47276951-47276969 chr11:47276953-47276968 chr11:47276953-47276968 chr11:47276952-47276967 chr11:47276953-47276967 chr11:47276954-47276966 chr11:47276954-47276966 chr11:47276953-47276966
6	SP1	chr11:47276254-47277065	HepG2	liver:	n/a	chr11:47276307-47276321
7	POLR2A	chr11:47276165-47276837	HUVEC	blood vessel:	n/a	n/a
8	FOXP2	chr11:47276340-47276824	PFSK-1	brain:	n/a	n/a
9	ELF1	chr11:47276298-47276762	HepG2	liver:	n/a	chr11:47276547-47276558 chr11:47276546-47276559
10	POLR2A	chr11:47276037-47277064	PFSK-1	brain:	n/a	n/a
11	FOXP2	chr11:47276268-47276827	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr11:47276303-47276809	HUVEC	blood vessel:	n/a	n/a
13	HEY1	chr11:47276241-47276896	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:47276250-47276991	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr11:47276304-47276974	HepG2	liver:	n/a	n/a
16	REST	chr11:47276201-47276731	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr11:47276306-47276885	HepG2	liver:	n/a	n/a
18	MYBL2	chr11:47276259-47276951	HepG2	liver:	n/a	n/a
19	ELF1	chr11:47276332-47276737	HepG2	liver:	n/a	chr11:47276547-47276558 chr11:47276546-47276559
20	MBD4	chr11:47276237-47277062	HepG2	liver:	n/a	n/a
21	RXRA	chr11:47276293-47276791	SK-N-SH	brain:	n/a	chr11:47276535-47276542
22	SPI1	chr11:47276243-47276776	HL-60	blood:	n/a	chr11:47276326-47276333
23	NFIC	chr11:47276255-47276765	HepG2	liver:	n/a	n/a
24	MBD4	chr11:47276327-47276757	HepG2	liver:	n/a	n/a
25	HEY1	chr11:47276189-47276950	HepG2	liver:	n/a	n/a
26	RXRA	chr11:47276273-47276801	HepG2	liver:	n/a	chr11:47276535-47276542
27	MAZ	chr11:47275226-47277002	IMR90	lung:	n/a	chr11:47276524-47276533 chr11:47275359-47275368
28	NFIC	chr11:47276304-47276996	HepG2	liver:	n/a	n/a
29	MYBL2	chr11:47276176-47277150	HepG2	liver:	n/a	n/a
30	POLR2A	chr11:47276207-47276883	HepG2	liver:	n/a	n/a
31	POLR2A	chr11:47276291-47276814	HepG2	liver:	n/a	n/a
32	POLR2A	chr11:47276320-47276669	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr11:47275834-47277056	HepG2	liver:	n/a	n/a
34	RXRA	chr11:47276177-47276913	HepG2	liver:	n/a	chr11:47276535-47276542
35	CEBPB	chr11:47276163-47276363	IMR90	lung:	n/a	chr11:47276244-47276255 chr11:47276245-47276256
36	TAF1	chr11:47276254-47276863	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47236362..47238989-chr11:47273774..47276751,3	K562	blood:
2	chr11:47274831..47277970-chr11:47278025..47280120,3	K562	blood:
3	chr11:47273867..47276931-chr11:47289002..47291937,3	MCF-7	breast:
4	chr11:47206818..47208802-chr11:47275094..47276860,2	MCF-7	breast:
5	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
6	chr11:47269243..47272486-chr11:47273981..47276768,5	MCF-7	breast:
7	chr11:47275155..47277753-chr11:47277972..47280489,3	MCF-7	breast:
8	chr11:47275538..47277558-chr11:47290062..47292106,2	K562	blood:
9	chr11:47268932..47273259-chr11:47273972..47277777,9	K562	blood:

Variant related genes	Relation type
NR1H3	TF binding region
ENSG00000110514	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10501321	0.89[EUR][1000 genomes]
rs1052373	0.85[EUR][1000 genomes]
rs1055510	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10742799	0.89[EUR][1000 genomes]
rs10742801	0.86[EUR][1000 genomes]
rs10838681	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10838684	0.90[EUR][1000 genomes]
rs10838690	0.88[EUR][1000 genomes]
rs10838691	0.86[EUR][1000 genomes]
rs10838692	0.86[EUR][1000 genomes]
rs10838693	0.86[EUR][1000 genomes]
rs11039156	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039166	0.88[EUR][1000 genomes]
rs11039167	0.84[EUR][1000 genomes]
rs12575456	0.88[EUR][1000 genomes]
rs1375688	0.88[EUR][1000 genomes]
rs1449627	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2013867	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2167079	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279239	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs326214	0.89[EUR][1000 genomes]
rs326222	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35677603	0.83[ASN][1000 genomes]
rs35879051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758669	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3758672	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3758673	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3781621	0.88[EUR][1000 genomes]
rs3781622	0.86[EUR][1000 genomes]
rs3816725	0.88[EUR][1000 genomes]
rs3847502	0.88[EUR][1000 genomes]
rs4647757	0.80[AFR][1000 genomes]
rs4752822	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752824	0.88[EUR][1000 genomes]
rs4752825	0.86[EUR][1000 genomes]
rs4752973	0.88[AFR][1000 genomes]
rs4752980	0.88[EUR][1000 genomes]
rs61896050	0.88[EUR][1000 genomes]
rs6485746	0.84[EUR][1000 genomes]
rs7109147	0.84[EUR][1000 genomes]
rs7109203	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7120118	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7120957	0.88[EUR][1000 genomes]
rs7124955	0.88[EUR][1000 genomes]
rs7127907	0.88[EUR][1000 genomes]
rs7129661	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7395581	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7940809	0.88[EUR][1000 genomes]
rs830085	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs901746	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs59663860	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs59663860	PACSIN3	cis	Esophagus Mucosa	GTEx
rs59663860	ACP2	cis	Thyroid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47271000-47280800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47271200-47276600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:47271400-47276400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr11:47271400-47276400	Weak transcription	Gastric	stomach
5	chr11:47271400-47276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:47271400-47276600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:47271400-47278600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:47271400-47278600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:47271400-47278600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:47271400-47278600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:47271400-47278600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:47271400-47278800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:47271400-47278800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr11:47271400-47278800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:47271400-47278800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr11:47271400-47278800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:47271400-47278800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:47271400-47278800	Weak transcription	Esophagus	oesophagus
19	chr11:47271400-47279000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:47271400-47279000	Weak transcription	Fetal Brain Female	brain
21	chr11:47271400-47279000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr11:47271400-47279200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr11:47271400-47281000	Weak transcription	Thymus	Thymus
24	chr11:47271400-47281200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:47271400-47281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr11:47271400-47281200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:47271400-47281200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:47271600-47279000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr11:47272000-47278600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:47272400-47286400	Weak transcription	Dnd41	blood
31	chr11:47274600-47277000	Enhancers	Lung	lung
32	chr11:47274800-47276600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr11:47274800-47276800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:47274800-47277000	Enhancers	Hela-S3	cervix
35	chr11:47275000-47276400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:47275000-47276400	Enhancers	Colonic Mucosa	Colon
37	chr11:47275000-47276400	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr11:47275000-47276600	Enhancers	Liver	Liver
39	chr11:47275000-47276600	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr11:47275000-47276800	Enhancers	HSMMtube	muscle
41	chr11:47275000-47277000	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr11:47275000-47277000	Enhancers	Left Ventricle	heart
43	chr11:47275000-47277000	Enhancers	Pancreas	Pancrea
44	chr11:47275000-47277000	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr11:47275000-47277000	Enhancers	Small Intestine	intestine
46	chr11:47275000-47277000	Enhancers	Stomach Mucosa	stomach
47	chr11:47275000-47277200	Flanking Active TSS	HepG2	liver
48	chr11:47275200-47276600	Enhancers	Fetal Thymus	thymus
49	chr11:47275200-47276800	Enhancers	Right Ventricle	heart
50	chr11:47275200-47276800	Enhancers	A549	lung

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