Variant report

Variant	rs11605125
Chromosome Location	chr11:65211019-65211020
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	POLR2A	chr11:65209087-65217647	Hela-S3	cervix:	n/a	n/a
2	CHD1	chr11:65183014-65218224	IMR90	lung:	n/a	chr11:65189696-65189706 chr11:65213009-65213016
3	POLR2A	chr11:65210479-65211170	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr11:65188590-65214677	MCF-7	breast:	n/a	n/a
5	POLR2A	chr11:65210269-65214714	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:65210258-65217283	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr11:65188505-65217165	ProgFib	skin:	n/a	n/a
8	RELA	chr11:65210589-65211317	GM18951	blood:	n/a	chr11:65211035-65211044 chr11:65211035-65211044
9	EBF1	chr11:65210871-65211319	GM12878	blood:	n/a	chr11:65211029-65211040
10	POLR2A	chr11:65209166-65217513	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr11:65210942-65211695	HCT-116	colon:	n/a	n/a
12	POLR2A	chr11:65210519-65212209	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:65210270-65214884	K562	blood:	n/a	n/a
14	POLR2A	chr11:65210354-65214911	HepG2	liver:	n/a	n/a
15	MEF2A	chr11:65210898-65211310	GM12878	blood:	n/a	n/a
16	NFYA	chr11:65210998-65211120	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr11:65210411-65211477	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr11:65210974-65211773	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:65210928-65211396	GM12891	blood:	n/a	n/a
20	BCL3	chr11:65210717-65211475	GM12878	blood:	n/a	n/a
21	POLR2A	chr11:65210370-65215342	GM12878	blood:	n/a	n/a
22	RUNX3	chr11:65210264-65212047	GM12878	blood:	n/a	chr11:65210387-65210396 chr11:65211096-65211105 chr11:65211096-65211105 chr11:65210387-65210396
23	POLR2A	chr11:65210230-65214884	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr11:65210903-65211278	GM12878	blood:	n/a	chr11:65211040-65211048
25	RELA	chr11:65210605-65211404	GM12891	blood:	n/a	chr11:65211035-65211044 chr11:65211035-65211044
26	RELA	chr11:65210846-65211298	GM10847	blood:	n/a	chr11:65211035-65211044 chr11:65211035-65211044
27	POLR2A	chr11:65210393-65214776	A549	lung:	n/a	n/a
28	IKZF1	chr11:65210940-65211338	GM12878	blood:	n/a	n/a
29	POLR2A	chr11:65210278-65216923	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr11:65210237-65214917	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr11:65204679-65217682	SK-N-SH	brain:	n/a	n/a
32	ELK4	chr11:65210430-65213662	HEK293	kidney:	n/a	chr11:65212423-65212432
33	POLR2A	chr11:65190093-65217195	HepG2	liver:	n/a	n/a
34	POLR2A	chr11:65210280-65214911	HepG2	liver:	n/a	n/a
35	POLR2A	chr11:65210245-65214608	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr11:65210581-65211158	HepG2	liver:	n/a	n/a
37	POU2F2	chr11:65210893-65211343	GM12891	blood:	n/a	n/a
38	FOXM1	chr11:65210634-65211543	GM12878	blood:	n/a	n/a
39	RELA	chr11:65210857-65211336	GM12892	blood:	n/a	chr11:65211035-65211044 chr11:65211035-65211044
40	POLR2A	chr11:65210337-65216578	K562	blood:	n/a	n/a
41	MTA3	chr11:65210367-65211722	GM12878	blood:	n/a	n/a
42	POLR2A	chr11:65210990-65211120	A549	lung:	n/a	n/a
43	POLR2A	chr11:65210271-65214850	K562	blood:	n/a	n/a
44	HEY1	chr11:65210332-65211110	HepG2	liver:	n/a	n/a
45	RELA	chr11:65210564-65211430	GM15510	blood:	n/a	chr11:65211035-65211044 chr11:65211035-65211044
46	POLR2A	chr11:65211015-65211458	GM12892	blood:	n/a	n/a
47	POLR2A	chr11:65210954-65212418	GM12891	blood:	n/a	n/a
48	POLR2A	chr11:65210667-65211670	GM19099	blood:	n/a	n/a
49	PML	chr11:65210369-65211820	GM12878	blood:	n/a	n/a
50	NFATC1	chr11:65210229-65211735	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
2	chr11:65210674..65211237-chr5:70751224..70751919,2	Hela-S3	cervix:
3	chr1:149222801..149224647-chr11:65210100..65211925,2	MCF-7	breast:

Variant related genes	Relation type
NEAT1	TF binding region
ENSG00000145734	Chromatin interaction
ENSG00000270526	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000173727	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11602839	1.00[CEU][hapmap]
rs1194758	0.87[CEU][hapmap]
rs1787666	0.87[CEU][hapmap]
rs2073801	0.85[CEU][hapmap]
rs2904976	0.85[CEU][hapmap]
rs550015	0.85[CEU][hapmap]
rs580933	1.00[CEU][hapmap]
rs616599	0.87[CEU][hapmap]
rs666834	0.85[CEU][hapmap]
rs673753	1.00[CEU][hapmap]
rs686320	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
15	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers 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	949 gene(s)	inside rSNPs	diseases
16	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	946 gene(s)	inside rSNPs	diseases
17	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
18	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription 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	961 gene(s)	inside rSNPs	diseases
19	nsv541075	chr11:65210592-65331136	Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	620 gene(s)	inside rSNPs	diseases
20	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11605125	PLCB3	cis	cerebellum	SCAN
rs11605125	MUS81	cis	parietal	SCAN
rs11605125	SLC22A11	cis	parietal	SCAN
rs11605125	POLA2	cis	parietal	SCAN
rs11605125	RAB3IL1	cis	cerebellum	SCAN
rs11605125	SLC25A45	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65198000-65216000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:65200600-65211600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
3	chr11:65200600-65214200	Strong transcription	NH-A	brain
4	chr11:65201600-65211600	Genic enhancers	Brain Substantia Nigra	brain
5	chr11:65202600-65214400	Genic enhancers	A549	lung
6	chr11:65203200-65211600	Strong transcription	HUVEC	blood vessel
7	chr11:65203400-65212200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr11:65205200-65214400	Genic enhancers	Placenta	Placenta
9	chr11:65205400-65211600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr11:65205400-65212400	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr11:65205600-65214800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:65205600-65217600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr11:65206200-65211200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:65206200-65211200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:65206200-65212400	Genic enhancers	Duodenum Mucosa	Duodenum
16	chr11:65206400-65213000	Genic enhancers	Osteobl	bone
17	chr11:65206600-65214400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:65206600-65222000	Weak transcription	Fetal Kidney	kidney
19	chr11:65206800-65211400	Enhancers	Primary B cells from peripheral blood	blood
20	chr11:65206800-65212800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:65207000-65211200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr11:65207000-65211400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr11:65207600-65211200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:65207600-65211400	Genic enhancers	Colon Smooth Muscle	Colon
25	chr11:65207800-65211200	Enhancers	Fetal Thymus	thymus
26	chr11:65207800-65211400	Genic enhancers	Left Ventricle	heart
27	chr11:65207800-65212400	Enhancers	Primary hematopoietic stem cells	blood
28	chr11:65207800-65214600	Genic enhancers	NHLF	lung
29	chr11:65208000-65212800	Genic enhancers	Rectal Mucosa Donor 29	rectum
30	chr11:65208200-65214600	Genic enhancers	Adipose Nuclei	Adipose
31	chr11:65208400-65211200	Enhancers	Fetal Heart	heart
32	chr11:65208400-65211600	Genic enhancers	HSMM	muscle
33	chr11:65208600-65214400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:65208800-65211200	Weak transcription	Primary T cells from cord blood	blood
35	chr11:65208800-65212200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr11:65208800-65214200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:65209000-65212200	Enhancers	Primary B cells from cord blood	blood
38	chr11:65209000-65217400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:65209200-65211800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:65209200-65212200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
41	chr11:65209200-65212200	Genic enhancers	Brain Inferior Temporal Lobe	brain
42	chr11:65209200-65213800	Genic enhancers	Pancreas	Pancrea
43	chr11:65209200-65214400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:65209200-65214400	Genic enhancers	Fetal Muscle Leg	muscle
45	chr11:65209400-65211200	Genic enhancers	Gastric	stomach
46	chr11:65209400-65211400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr11:65209400-65211400	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr11:65209400-65211600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:65209400-65211600	Genic enhancers	Brain Anterior Caudate	brain
50	chr11:65209400-65211600	Genic enhancers	Ovary	ovary

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