Variant report

Variant	rs3782089
Chromosome Location	chr11:65336819-65336820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr11:65336628-65338443	A549	lung:	n/a	n/a
2	POLR2A	chr11:65336533-65338314	GM12892	blood:	n/a	n/a
3	POLR2A	chr11:65336528-65338307	SK-N-MC	brain:	n/a	n/a
4	MAX	chr11:65336701-65338565	K562	blood:	n/a	n/a
5	POLR2A	chr11:65336527-65338249	GM12878	blood:	n/a	n/a
6	MAX	chr11:65336646-65338322	HCT-116	colon:	n/a	n/a
7	ELF1	chr11:65336757-65337281	K562	blood:	n/a	n/a
8	SIX5	chr11:65336722-65338316	A549	lung:	n/a	n/a
9	HCFC1	chr11:65335547-65338561	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr11:65336337-65338250	A549	lung:	n/a	chr11:65337902-65337915 chr11:65336529-65336537
11	POLR2A	chr11:65336619-65338160	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:65336699-65338371	K562	blood:	n/a	n/a
13	POLR2A	chr11:65336690-65336889	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:65336472-65338317	HepG2	liver:	n/a	n/a
15	MXI1	chr11:65336214-65338802	SK-N-SH	brain:	n/a	chr11:65337705-65337720
16	POLR2A	chr11:65336567-65338317	GM12892	blood:	n/a	n/a
17	REST	chr11:65336766-65338523	H1-neurons	neurons:	n/a	chr11:65337562-65337575 chr11:65337273-65337280
18	MAX	chr11:65336614-65338387	MCF-7	breast:	n/a	n/a
19	MAZ	chr11:65336306-65338566	IMR90	lung:	n/a	n/a
20	MTA3	chr11:65336656-65338288	GM12878	blood:	n/a	n/a
21	MAX	chr11:65336711-65338339	A549	lung:	n/a	n/a
22	NRF1	chr11:65336494-65338145	SK-N-SH	brain:	n/a	chr11:65337501-65337512 chr11:65337501-65337515 chr11:65337498-65337512 chr11:65337259-65337273 chr11:65337501-65337512 chr11:65337566-65337575 chr11:65337503-65337512
23	MAX	chr11:65336813-65338161	GM12878	blood:	n/a	n/a
24	CREB1	chr11:65336761-65338425	HepG2	liver:	n/a	n/a
25	JUN	chr11:65336260-65338579	K562	blood:	n/a	n/a
26	MAX	chr11:65336767-65338217	NB4	blood:	n/a	n/a
27	MXI1	chr11:65336811-65338180	GM12878	blood:	n/a	chr11:65337705-65337720

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65185945..65193560-chr11:65336627..65344485,19	K562	blood:
2	chr11:65336349..65338989-chr11:65428353..65432348,4	MCF-7	breast:
3	chr11:65182317..65198249-chr11:65333937..65346467,45	MCF-7	breast:
4	chr11:65335401..65344755-chr11:65379602..65385163,20	K562	blood:
5	chr11:65262109..65269742-chr11:65336183..65344125,16	MCF-7	breast:
6	chr11:65263786..65274103-chr11:65335962..65346813,28	MCF-7	breast:
7	chr11:65336222..65339291-chr11:65623626..65626992,4	K562	blood:
8	chr11:65335492..65337071-chr17:7737574..7739676,2	MCF-7	breast:
9	chr11:65336061..65346997-chr11:65371025..65390625,42	MCF-7	breast:
10	chr11:65336026..65338505-chr11:65655594..65658699,3	MCF-7	breast:
11	chr11:65149449..65149970-chr11:65336591..65337539,2	K562	blood:
12	chr11:65264659..65267625-chr11:65336211..65338117,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LTBP3-1	chr11:65335953-65337894	ENSG00000260233.1
2	lnc-LTBP3-1	chr11:65333533-65337942	NONHSAT022168
3	lnc-LTBP3-1	chr11:65336691-65337884	NONHSAT022169

No data

Variant related genes	Relation type
FAM89B	TF binding region
SSSCA1	TF binding region
ENSG00000162241	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000172757	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10896018	1.00[YRI][hapmap]
rs11545200	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11600543	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11602375	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11604369	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11605810	0.92[EUR][1000 genomes]
rs11605937	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1194337	0.82[EUR][1000 genomes]
rs12799784	0.94[EUR][1000 genomes]
rs34789990	0.80[EUR][1000 genomes]
rs35111506	0.88[EUR][1000 genomes]
rs35138901	0.84[EUR][1000 genomes]
rs4601790	0.82[ASW][hapmap];1.00[YRI][hapmap]
rs71462347	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7935877	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
11	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
12	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
13	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
14	nsv897730	chr11:65302893-65376484	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
15	nsv468599	chr11:65335705-65427346	ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
16	nsv555213	chr11:65335705-65427346	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
17	nsv897732	chr11:65335705-65427346	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
18	nsv468600	chr11:65335705-65431360	Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
19	nsv555214	chr11:65335705-65431360	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
20	nsv897733	chr11:65335705-65431360	Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
21	nsv897734	chr11:65335705-65436888	Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
22	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
23	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' 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	227 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	20881960	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3782089	RNASEH2C	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65336200-65337000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr11:65336200-65337000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:65336200-65337000	Flanking Active TSS	NHLF	lung
4	chr11:65336200-65337200	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr11:65336200-65337200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr11:65336200-65337200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:65336200-65337200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr11:65336200-65337200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:65336200-65337200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:65336200-65337200	Flanking Active TSS	Hela-S3	cervix
11	chr11:65336200-65337400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr11:65336200-65337400	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr11:65336200-65337400	Flanking Active TSS	Fetal Brain Male	brain
14	chr11:65336200-65337400	Flanking Active TSS	Rectal Smooth Muscle	rectum
15	chr11:65336200-65337400	Flanking Active TSS	HMEC	breast
16	chr11:65336200-65337400	Flanking Active TSS	K562	blood
17	chr11:65336200-65337600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr11:65336200-65337600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:65336200-65337600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr11:65336200-65337600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr11:65336400-65337000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:65336400-65337000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:65336400-65337000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr11:65336400-65337000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:65336400-65337000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:65336400-65337000	Flanking Active TSS	Brain Angular Gyrus	brain
27	chr11:65336400-65337000	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr11:65336400-65337000	Flanking Active TSS	Colonic Mucosa	Colon
29	chr11:65336400-65337000	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr11:65336400-65337000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr11:65336400-65337000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
32	chr11:65336400-65337000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr11:65336400-65337000	Flanking Active TSS	Thymus	Thymus
34	chr11:65336400-65337000	Flanking Active TSS	HSMM	muscle
35	chr11:65336400-65337000	Flanking Active TSS	NHDF-Ad	bronchial
36	chr11:65336400-65337200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:65336400-65337200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:65336400-65337200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr11:65336400-65337200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr11:65336400-65337200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:65336400-65337200	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr11:65336400-65337200	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr11:65336400-65337200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr11:65336400-65337200	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr11:65336400-65337200	Flanking Active TSS	Fetal Heart	heart
46	chr11:65336400-65337200	Flanking Active TSS	Fetal Lung	lung
47	chr11:65336400-65337200	Flanking Active TSS	Pancreas	Pancrea
48	chr11:65336400-65337200	Flanking Active TSS	NHEK	skin
49	chr11:65336400-65337400	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr11:65336400-65337400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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