Variant report

Variant	rs4244811
Chromosome Location	chr11:65320780-65320781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr11:65320504-65320991	HL-60	blood:	n/a	chr11:65320773-65320786
2	POLR2A	chr11:65320776-65321370	K562	blood:	n/a	n/a
3	TAL1	chr11:65320707-65320829	K562	blood:	n/a	n/a
4	MAZ	chr11:65320658-65321447	K562	blood:	n/a	n/a
5	POLR2A	chr11:65320697-65321667	K562	blood:	n/a	n/a
6	RCOR1	chr11:65320679-65321355	K562	blood:	n/a	n/a
7	POLR2A	chr11:65320683-65321483	SK-N-MC	brain:	n/a	n/a
8	IRF1	chr11:65320694-65321322	K562	blood:	n/a	n/a
9	SPI1	chr11:65320629-65320808	K562	blood:	n/a	chr11:65320773-65320786
10	CTCF	chr11:65320680-65320830	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65319428..65321509-chr11:65390618..65393221,2	MCF-7	breast:
2	chr11:65264479..65268560-chr11:65318003..65330456,22	MCF-7	breast:
3	chr11:65320341..65322130-chr11:65626386..65628197,2	K562	blood:
4	chr11:65190162..65194738-chr11:65316952..65321274,6	K562	blood:
5	chr11:65184371..65196984-chr11:65316952..65328208,29	K562	blood:

No data

Variant related genes	Relation type
LTBP3	TF binding region
ENSG00000172732	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000251562	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10896015	0.80[JPT][hapmap]
rs10896016	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1111934	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11227221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151517	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11601767	0.92[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11604423	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11607147	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1194076	0.80[JPT][hapmap]
rs12270054	0.80[JPT][hapmap]
rs12790095	0.83[EUR][1000 genomes]
rs1787663	0.80[JPT][hapmap]
rs3782091	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs600231	0.88[MKK][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv897729	chr11:65302893-65322548	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
19	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4244811	INCENP	cis	cerebellum	SCAN
rs4244811	TTC9C	cis	parietal	SCAN
rs4244811	CDK2AP2	cis	cerebellum	SCAN
rs4244811	LTBP3	cis	cerebellum	SCAN
rs4244811	NEAT1	cis	Esophagus Muscularis	GTEx
rs4244811	BBS1	cis	parietal	SCAN
rs4244811	EIF1AD	cis	cerebellum	SCAN
rs4244811	NEAT1	cis	Nerve Tibial	GTEx
rs4244811	TPCN2	cis	parietal	SCAN
rs4244811	TncRNA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65307200-65322600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:65309200-65322200	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr11:65309200-65323000	Weak transcription	Psoas Muscle	Psoas
4	chr11:65309400-65323000	Weak transcription	Right Atrium	heart
5	chr11:65309800-65322200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:65310200-65320800	Strong transcription	Brain Cingulate Gyrus	brain
7	chr11:65310400-65322000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:65310800-65324000	Weak transcription	Fetal Kidney	kidney
9	chr11:65313000-65320800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:65314600-65321000	Strong transcription	Fetal Stomach	stomach
11	chr11:65314800-65321600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:65314800-65322800	Weak transcription	NHEK	skin
13	chr11:65315200-65321200	Weak transcription	Fetal Brain Male	brain
14	chr11:65315400-65321200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr11:65316600-65320800	Strong transcription	Brain Hippocampus Middle	brain
16	chr11:65316600-65321200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:65317000-65322400	Weak transcription	HSMMtube	muscle
18	chr11:65317600-65321400	Weak transcription	Fetal Brain Female	brain
19	chr11:65318000-65321000	Genic enhancers	Placenta	Placenta
20	chr11:65318400-65320800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:65318400-65320800	Genic enhancers	Spleen	Spleen
22	chr11:65318400-65321600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:65318400-65321800	Strong transcription	NHLF	lung
24	chr11:65318400-65322000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:65318400-65323000	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr11:65318600-65321400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:65318600-65322400	Enhancers	Primary B cells from peripheral blood	blood
28	chr11:65318600-65323600	Genic enhancers	Fetal Muscle Leg	muscle
29	chr11:65318600-65325800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:65318800-65322000	Enhancers	Primary B cells from cord blood	blood
31	chr11:65318800-65322400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr11:65318800-65324600	Enhancers	Primary hematopoietic stem cells	blood
33	chr11:65319000-65321000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr11:65319000-65321200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr11:65319000-65321800	Strong transcription	Brain Anterior Caudate	brain
36	chr11:65319000-65323400	Genic enhancers	Fetal Intestine Small	intestine
37	chr11:65319000-65324200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:65319000-65324600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr11:65319000-65324600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr11:65319200-65320800	Enhancers	K562	blood
41	chr11:65319200-65321000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:65319200-65321200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr11:65319200-65323200	Weak transcription	Fetal Heart	heart
44	chr11:65319400-65321000	Enhancers	Primary T cells from cord blood	blood
45	chr11:65319400-65321000	Enhancers	Primary T cells fromperipheralblood	blood
46	chr11:65319400-65321000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr11:65319400-65321400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:65319400-65323400	Weak transcription	Brain Substantia Nigra	brain
49	chr11:65319600-65321000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr11:65319600-65321400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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