Variant report

Variant	rs11604423
Chromosome Location	chr11:65345828-65345829
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	MTA3	chr11:65340869-65345892	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:65345784-65345830	K562	blood:	n/a	n/a
3	POLR2A	chr11:65340616-65350223	K562	blood:	n/a	n/a
4	MAZ	chr11:65339391-65345893	IMR90	lung:	n/a	chr11:65343890-65343900 chr11:65341903-65341913 chr11:65343762-65343772 chr11:65344304-65344314 chr11:65340456-65340466
5	POLR2A	chr11:65344071-65349042	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65343882..65346090-chr11:65625521..65627061,2	MCF-7	breast:
2	chr11:65182317..65198249-chr11:65333937..65346467,45	MCF-7	breast:
3	chr11:65263786..65274103-chr11:65335962..65346813,28	MCF-7	breast:
4	chr11:65344954..65347846-chr11:65406029..65407585,2	MCF-7	breast:
5	chr11:65336061..65346997-chr11:65371025..65390625,42	MCF-7	breast:
6	chr11:65343176..65345868-chr11:65665917..65668139,2	K562	blood:
7	chr11:65342557..65345868-chr11:65665917..65668139,3	K562	blood:
8	chr11:65343451..65346634-chr11:65622563..65625144,3	K562	blood:
9	chr11:65341009..65346216-chr11:65370852..65374605,4	K562	blood:

Variant related genes	Relation type
EHBP1L1	TF binding region
ENSG00000173327	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000213445	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000175592	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10896016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1111934	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11227221	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1151517	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11601767	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11607147	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790095	0.83[EUR][1000 genomes]
rs3782091	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244811	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	nsv897737	chr11:65337714-65361765	Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
24	nsv897738	chr11:65337714-65380248	Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
25	nsv897739	chr11:65337714-65388300	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
26	nsv897740	chr11:65338589-65371604	Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
27	nsv897741	chr11:65338589-65376484	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
28	nsv897742	chr11:65338589-65380248	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
29	nsv897743	chr11:65338589-65382564	Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
30	nsv897744	chr11:65339099-65359435	Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Enhancers 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	37 gene(s)	inside rSNPs	diseases
31	nsv897745	chr11:65339099-65367253	Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
32	esv2761680	chr11:65344328-65391317	Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11604423	NEAT1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65342800-65346400	Enhancers	Fetal Brain Male	brain
2	chr11:65343800-65346000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
3	chr11:65343800-65346400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:65344000-65346200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:65344000-65346200	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr11:65344200-65346400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:65344200-65346400	Weak transcription	Ovary	ovary
8	chr11:65344200-65346600	Enhancers	Fetal Heart	heart
9	chr11:65344200-65351400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:65344200-65351800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:65344200-65352000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:65344400-65346400	Enhancers	Fetal Brain Female	brain
13	chr11:65344400-65346800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:65344400-65351600	Weak transcription	Brain Substantia Nigra	brain
15	chr11:65344600-65346200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:65344600-65346600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr11:65344600-65351800	Weak transcription	Brain Angular Gyrus	brain
18	chr11:65344800-65346000	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
19	chr11:65344800-65348400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:65344800-65348600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:65345000-65346200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:65345000-65347400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:65345200-65346000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:65345200-65346000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
25	chr11:65345200-65346000	Flanking Active TSS	Psoas Muscle	Psoas
26	chr11:65345200-65346000	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr11:65345200-65346000	Enhancers	Dnd41	blood
28	chr11:65345200-65346000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr11:65345200-65346200	Enhancers	HepG2	liver
30	chr11:65345200-65346400	Enhancers	Gastric	stomach
31	chr11:65345200-65346600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr11:65345400-65346000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr11:65345400-65346000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:65345400-65346000	Enhancers	Fetal Intestine Large	intestine
35	chr11:65345400-65346200	Enhancers	Liver	Liver
36	chr11:65345400-65346200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
37	chr11:65345400-65346400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr11:65345400-65346400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr11:65345400-65346400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr11:65345400-65346400	Genic enhancers	Thymus	Thymus
41	chr11:65345400-65346400	Enhancers	A549	lung
42	chr11:65345400-65346600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:65345400-65346600	Genic enhancers	Lung	lung
44	chr11:65345400-65346800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:65345400-65346800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr11:65345400-65346800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
47	chr11:65345400-65347200	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr11:65345400-65347400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:65345400-65347400	Weak transcription	Pancreas	Pancrea
50	chr11:65345400-65351600	Weak transcription	Brain Anterior Caudate	brain

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