Variant report

Variant	rs3741384
Chromosome Location	chr11:65211505-65211506
allele	C/T
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	chr11:65211071-65212427	A549	lung:	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	chr11:65211480-65212497	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr11:65188505-65217165	ProgFib	skin:	n/a	n/a
9	POU2F2	chr11:65211447-65211776	GM12891	blood:	n/a	n/a
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	POLR2A	chr11:65211500-65211776	A549	lung:	n/a	n/a
16	CEBPB	chr11:65211346-65211540	HepG2	liver:	n/a	n/a
17	ZNF263	chr11:65211187-65211901	HEK293-T-REx	kidney:	n/a	n/a
18	POLR2A	chr11:65210974-65211773	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:65210370-65215342	GM12878	blood:	n/a	n/a
20	RUNX3	chr11:65210264-65212047	GM12878	blood:	n/a	chr11:65210387-65210396 chr11:65211096-65211105 chr11:65211096-65211105 chr11:65210387-65210396
21	KAP1	chr11:65211285-65211544	U2OS	brain:	n/a	n/a
22	POLR2A	chr11:65210230-65214884	Hela-S3	cervix:	n/a	n/a
23	CEBPB	chr11:65211300-65211660	IMR90	lung:	n/a	n/a
24	POLR2A	chr11:65210393-65214776	A549	lung:	n/a	n/a
25	POLR2A	chr11:65211418-65211819	GM12891	blood:	n/a	n/a
26	POLR2A	chr11:65211089-65211700	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:65211045-65214573	GM12892	blood:	n/a	n/a
28	POLR2A	chr11:65210278-65216923	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr11:65210237-65214917	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr11:65204679-65217682	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr11:65211257-65211599	HCT-116	colon:	n/a	n/a
32	CTCF	chr11:65211420-65211570	HCPEpiC	choroid plexus:	n/a	n/a
33	JUND	chr11:65211184-65214537	SK-N-SH	brain:	n/a	chr11:65213399-65213407 chr11:65211291-65211300
34	ELK4	chr11:65210430-65213662	HEK293	kidney:	n/a	chr11:65212423-65212432
35	POLR2A	chr11:65190093-65217195	HepG2	liver:	n/a	n/a
36	POLR2A	chr11:65210280-65214911	HepG2	liver:	n/a	n/a
37	POLR2A	chr11:65210245-65214608	HUVEC	blood vessel:	n/a	n/a
38	FOXM1	chr11:65210634-65211543	GM12878	blood:	n/a	n/a
39	CHD2	chr11:65211141-65212362	K562	blood:	n/a	n/a
40	POLR2A	chr11:65210337-65216578	K562	blood:	n/a	n/a
41	MTA3	chr11:65210367-65211722	GM12878	blood:	n/a	n/a
42	POLR2A	chr11:65210271-65214850	K562	blood:	n/a	n/a
43	HEY1	chr11:65211402-65212804	HepG2	liver:	n/a	n/a
44	POLR2A	chr11:65210954-65212418	GM12891	blood:	n/a	n/a
45	POLR2A	chr11:65210667-65211670	GM19099	blood:	n/a	n/a
46	PML	chr11:65210369-65211820	GM12878	blood:	n/a	n/a
47	NFATC1	chr11:65210229-65211735	GM12878	blood:	n/a	n/a
48	POLR2A	chr11:65211408-65211772	A549	lung:	n/a	n/a
49	POLR2A	chr11:65211246-65214771	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr11:65210613-65214407	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
2	chr1:149222801..149224647-chr11:65210100..65211925,2	MCF-7	breast:

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

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11602839	1.00[CHB][hapmap]
rs1205739	0.84[EUR][1000 genomes]
rs2073801	1.00[CHB][hapmap]
rs2239895	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2307264	1.00[AFR][1000 genomes]
rs2904976	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs34412377	1.00[AFR][1000 genomes]
rs34789990	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35111506	1.00[AFR][1000 genomes]
rs36009527	1.00[AFR][1000 genomes]
rs36085849	1.00[AFR][1000 genomes]
rs573864	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs666834	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs680413	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7925823	0.91[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]

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

No data

Chromatin state (count:110 , 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	chr11:65206200-65212400	Genic enhancers	Duodenum Mucosa	Duodenum
14	chr11:65206400-65213000	Genic enhancers	Osteobl	bone
15	chr11:65206600-65214400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:65206600-65222000	Weak transcription	Fetal Kidney	kidney
17	chr11:65206800-65212800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:65207800-65212400	Enhancers	Primary hematopoietic stem cells	blood
19	chr11:65207800-65214600	Genic enhancers	NHLF	lung
20	chr11:65208000-65212800	Genic enhancers	Rectal Mucosa Donor 29	rectum
21	chr11:65208200-65214600	Genic enhancers	Adipose Nuclei	Adipose
22	chr11:65208400-65211600	Genic enhancers	HSMM	muscle
23	chr11:65208600-65214400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:65208800-65212200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr11:65208800-65214200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:65209000-65212200	Enhancers	Primary B cells from cord blood	blood
27	chr11:65209000-65217400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:65209200-65211800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:65209200-65212200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr11:65209200-65212200	Genic enhancers	Brain Inferior Temporal Lobe	brain
31	chr11:65209200-65213800	Genic enhancers	Pancreas	Pancrea
32	chr11:65209200-65214400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:65209200-65214400	Genic enhancers	Fetal Muscle Leg	muscle
34	chr11:65209400-65211600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:65209400-65211600	Genic enhancers	Brain Anterior Caudate	brain
36	chr11:65209400-65211600	Genic enhancers	Ovary	ovary
37	chr11:65209400-65212400	Genic enhancers	Placenta Amnion	Placenta Amnion
38	chr11:65209400-65212800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr11:65209400-65212800	Genic enhancers	K562	blood
40	chr11:65209400-65213400	Enhancers	Right Atrium	heart
41	chr11:65209400-65214200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:65209400-65214400	Strong transcription	Thymus	Thymus
43	chr11:65209400-65214400	Genic enhancers	Spleen	Spleen
44	chr11:65209400-65214600	Genic enhancers	Fetal Muscle Trunk	muscle
45	chr11:65209600-65212200	Genic enhancers	Brain Hippocampus Middle	brain
46	chr11:65209600-65214600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:65209600-65214600	Genic enhancers	NHDF-Ad	bronchial
48	chr11:65209800-65211600	Genic enhancers	Fetal Stomach	stomach
49	chr11:65209800-65211600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
50	chr11:65209800-65211800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood

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