Variant report

Variant	rs11884118
Chromosome Location	chr2:47268113-47268114
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	MAX	chr2:47267490-47268348	HepG2	liver:	n/a	n/a
2	EP300	chr2:47267756-47268128	HepG2	liver:	n/a	n/a
3	MAZ	chr2:47266941-47268589	IMR90	lung:	n/a	chr2:47267355-47267365 chr2:47267353-47267366 chr2:47267355-47267365 chr2:47267355-47267364 chr2:47267354-47267365 chr2:47267350-47267369 chr2:47267353-47267366 chr2:47267354-47267365 chr2:47267354-47267365
4	TEAD4	chr2:47267726-47268252	HepG2	liver:	n/a	n/a
5	JUND	chr2:47267904-47268119	HepG2	liver:	n/a	n/a
6	HDAC2	chr2:47267719-47268188	HepG2	liver:	n/a	n/a
7	HNF4G	chr2:47267697-47268242	HepG2	liver:	n/a	chr2:47267983-47267998 chr2:47267984-47267997 chr2:47267984-47267999 chr2:47267984-47267992 chr2:47267985-47267997 chr2:47267985-47267997
8	HNF4G	chr2:47267741-47268200	HepG2	liver:	n/a	chr2:47267983-47267998 chr2:47267984-47267997 chr2:47267984-47267999 chr2:47267984-47267992 chr2:47267985-47267997 chr2:47267985-47267997
9	RAD21	chr2:47267877-47268145	HepG2	liver:	n/a	n/a
10	HNF4A	chr2:47267762-47268240	HepG2	liver:	n/a	chr2:47267983-47267998 chr2:47267984-47267997 chr2:47267983-47267998 chr2:47267984-47267992 chr2:47267985-47267997 chr2:47267985-47267997
11	EP300	chr2:47267459-47271977	SK-N-SH	brain:	n/a	chr2:47271431-47271438
12	MYBL2	chr2:47267662-47268375	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:47266497-47268572	IMR90	lung:	n/a	n/a
14	POLR2A	chr2:47267956-47268219	HepG2	liver:	n/a	n/a
15	MAX	chr2:47267812-47268131	HepG2	liver:	n/a	n/a
16	HNF4A	chr2:47267763-47268139	HepG2	liver:	n/a	chr2:47267983-47267998 chr2:47267984-47267997 chr2:47267983-47267998 chr2:47267984-47267992 chr2:47267985-47267997 chr2:47267985-47267997
17	EP300	chr2:47268094-47268591	SK-N-SH_RA	brain:	n/a	n/a
18	ZEB1	chr2:47267598-47268281	HepG2	liver:	n/a	chr2:47267937-47267948 chr2:47267914-47267925 chr2:47267937-47267948
19	ZEB1	chr2:47266291-47268643	HepG2	liver:	n/a	chr2:47267937-47267948 chr2:47267914-47267925 chr2:47266864-47266871 chr2:47267937-47267948
20	CHD1	chr2:47266937-47268572	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47267673..47270387-chr2:47397211..47399730,2	K562	blood:
2	chr2:47266042..47270456-chr2:47271373..47275642,6	K562	blood:
3	chr2:47266621..47268333-chr2:47402251..47405072,2	K562	blood:

Variant related genes	Relation type
ENSG00000233845	TF binding region
ENSG00000143933	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10495942	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11890603	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11901122	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13353361	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13423726	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17036119	1.00[LWK][hapmap]
rs17036138	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17481182	1.00[ASW][hapmap]
rs17541155	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17541307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3814037	0.81[AMR][1000 genomes]
rs55654462	0.91[AMR][1000 genomes]
rs56139747	0.91[AMR][1000 genomes]
rs56200787	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73929358	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7581528	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription 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 target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984532	chr2:47237908-47270533	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv528091	chr2:47249239-47273732	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11884118	PLOD1	trans	brain	seeQTL
rs11884118	DEDD2	trans	brain	seeQTL
rs11884118	PLOD3	trans	brain	seeQTL
rs11884118	MKLN1	trans	brain	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47234400-47283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:47236000-47278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:47245800-47268600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:47246000-47283800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:47246800-47281600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:47252000-47283400	Strong transcription	Thymus	Thymus
8	chr2:47255600-47273400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:47257000-47277000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:47258400-47268400	Genic enhancers	Fetal Thymus	thymus
11	chr2:47258400-47282600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:47259600-47295000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:47261800-47268600	Genic enhancers	NHLF	lung
14	chr2:47261800-47273600	Weak transcription	Fetal Brain Female	brain
15	chr2:47262000-47283400	Weak transcription	Fetal Brain Male	brain
16	chr2:47262000-47283600	Weak transcription	Small Intestine	intestine
17	chr2:47262400-47269000	Weak transcription	Brain Germinal Matrix	brain
18	chr2:47262600-47268200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:47262600-47268600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:47262600-47269200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:47262800-47268400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:47262800-47269000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:47262800-47269200	Genic enhancers	A549	lung
24	chr2:47262800-47269800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:47263000-47283200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:47263200-47268400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:47263200-47269000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:47263200-47269200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:47263400-47268400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:47263400-47270000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:47263400-47283200	Weak transcription	Fetal Kidney	kidney
32	chr2:47263600-47268200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:47263600-47268400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:47264000-47268600	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr2:47264200-47268600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:47264600-47269000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:47264800-47268600	Genic enhancers	Fetal Intestine Small	intestine
38	chr2:47265000-47273200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:47265000-47273400	Weak transcription	K562	blood
40	chr2:47265400-47268600	Genic enhancers	Primary monocytes fromperipheralblood	blood
41	chr2:47265400-47268800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:47265800-47268400	Genic enhancers	NHDF-Ad	bronchial
43	chr2:47265800-47268600	Genic enhancers	Lung	lung
44	chr2:47265800-47268800	Enhancers	Left Ventricle	heart
45	chr2:47265800-47269200	Weak transcription	Hela-S3	cervix
46	chr2:47266000-47268200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr2:47266000-47268400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:47266000-47268600	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:47266000-47268600	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr2:47266000-47268800	Enhancers	Right Ventricle	heart

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