Variant report

Variant	rs652501
Chromosome Location	chr11:65160145-65160146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65160102-65160456	K562	blood:	n/a	n/a
2	CTCF	chr11:65160134-65160249	MCF-7	breast:	n/a	n/a
3	ESR1	chr11:65159928-65160344	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr11:65159291-65160830	K562	blood:	n/a	n/a
5	POLR2A	chr11:65160128-65160157	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:65160135-65160169	HUVEC	blood vessel:	n/a	n/a
7	EP300	chr11:65159254-65160416	SK-N-SH	brain:	n/a	n/a
8	ESR1	chr11:65159999-65160314	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr11:65160111-65160251	MCF-7	breast:	n/a	n/a
10	CTCF	chr11:65160132-65160173	GM12892	blood:	n/a	n/a
11	CTCF	chr11:65160135-65160244	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr11:65160111-65160229	HepG2	liver:	n/a	n/a
13	ESR1	chr11:65160037-65160260	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr11:65160088-65160264	MCF-7	breast:	n/a	n/a
15	CTCF	chr11:65160124-65160252	MCF-7	breast:	n/a	n/a
16	CTCF	chr11:65160082-65160247	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65158047..65160155-chr11:65175954..65178054,2	MCF-7	breast:

No data

Variant related genes	Relation type
FRMD8	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs2073799	0.81[EUR][1000 genomes]
rs2073800	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930154	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs547221	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs578270	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs585210	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs651283	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs666194	0.82[GIH][hapmap]
rs681309	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs652501	NEAT1	cis	Muscle Skeletal	GTEx
rs652501	CDK2AP2	cis	cerebellum	SCAN
rs652501	HRASLS2	cis	parietal	SCAN
rs652501	NEAT1	cis	Nerve Tibial	GTEx
rs652501	SLC22A24	cis	parietal	SCAN
rs652501	TPCN2	cis	parietal	SCAN
rs652501	SDHAF2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65154800-65161000	Weak transcription	Aorta	Aorta
2	chr11:65154800-65164800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:65155000-65162000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:65155600-65161800	Genic enhancers	Spleen	Spleen
5	chr11:65155600-65162400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:65156000-65162200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:65156600-65169800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr11:65156600-65169800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:65157200-65161400	Weak transcription	Small Intestine	intestine
10	chr11:65157200-65182800	Weak transcription	Psoas Muscle	Psoas
11	chr11:65157400-65170800	Strong transcription	Thymus	Thymus
12	chr11:65157600-65167800	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:65157600-65169000	Weak transcription	Stomach Mucosa	stomach
14	chr11:65157800-65160800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr11:65157800-65164800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:65157800-65164800	Weak transcription	HepG2	liver
17	chr11:65157800-65170800	Weak transcription	K562	blood
18	chr11:65158000-65160400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr11:65158200-65160400	Strong transcription	Fetal Thymus	thymus
20	chr11:65158200-65160800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:65158200-65168400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:65158200-65170400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:65158400-65160200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr11:65158400-65161600	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:65158400-65167800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:65158400-65168000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:65158400-65169600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:65158600-65163000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr11:65158600-65164800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:65158600-65165400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:65158600-65167600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr11:65158600-65167600	Strong transcription	Fetal Intestine Large	intestine
33	chr11:65158600-65168000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr11:65158600-65170200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr11:65158600-65183200	Weak transcription	Fetal Brain Male	brain
36	chr11:65158600-65183400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:65158800-65160200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr11:65158800-65160200	Weak transcription	A549	lung
39	chr11:65158800-65160400	Weak transcription	Brain Anterior Caudate	brain
40	chr11:65158800-65160600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:65158800-65160800	Weak transcription	Brain Substantia Nigra	brain
42	chr11:65158800-65161000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:65158800-65162000	Weak transcription	Ovary	ovary
44	chr11:65158800-65162400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:65158800-65164000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:65158800-65164400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr11:65158800-65167000	Weak transcription	Hela-S3	cervix
48	chr11:65158800-65167400	Strong transcription	Colonic Mucosa	Colon
49	chr11:65158800-65168400	Strong transcription	Dnd41	blood
50	chr11:65158800-65172200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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