Variant report

Variant	rs12295516
Chromosome Location	chr11:62624931-62624932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62624507-62625160	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:62624662-62624943	K562	blood:	n/a	n/a
3	POLR2A	chr11:62617338-62625222	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:62618403-62625433	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:62617682-62625430	PFSK-1	brain:	n/a	n/a
6	CHD1	chr11:62624741-62625676	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:62624637-62625073	K562	blood:	n/a	n/a
8	ZNF384	chr11:62624918-62625642	GM12878	blood:	n/a	n/a
9	MAX	chr11:62624640-62625016	K562	blood:	n/a	n/a
10	POLR2A	chr11:62624500-62626198	H1-hESC	embryonic stem cell:	n/a	n/a
11	RCOR1	chr11:62624870-62625282	K562	blood:	n/a	n/a
12	POLR2A	chr11:62624826-62625256	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr11:62617286-62625531	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr11:62624506-62625177	K562	blood:	n/a	n/a
15	POLR2A	chr11:62617624-62625492	PFSK-1	brain:	n/a	n/a
16	NR2F2	chr11:62624570-62625009	K562	blood:	n/a	n/a
17	POLR2A	chr11:62624563-62625383	K562	blood:	n/a	n/a
18	HEY1	chr11:62618343-62624934	K562	blood:	n/a	n/a
19	POLR2A	chr11:62624505-62625398	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62597102..62625754-chr11:62640222..62672995,305	MCF-7	breast:
2	chr11:62474385..62478486-chr11:62621122..62625313,5	MCF-7	breast:
3	chr11:62493159..62495020-chr11:62623607..62625320,2	MCF-7	breast:
4	chr11:62565367..62576307-chr11:62617328..62626616,39	K562	blood:
5	chr11:62339984..62344096-chr11:62621681..62625316,4	K562	blood:
6	chr11:62473263..62476310-chr11:62622744..62625720,5	K562	blood:
7	chr11:62432496..62434344-chr11:62623258..62625470,4	K562	blood:
8	chr11:62492410..62497430-chr11:62621392..62625675,11	K562	blood:
9	chr11:62552943..62561747-chr11:62616572..62625876,31	K562	blood:
10	chr11:62614063..62631836-chr11:62641578..62658963,131	K562	blood:
11	chr11:62622571..62624950-chr17:56708103..56709921,2	MCF-7	breast:
12	chr11:62339818..62342516-chr11:62622172..62625340,3	MCF-7	breast:
13	chr11:62492343..62497215-chr11:62619514..62625025,15	MCF-7	breast:
14	chr11:62388618..62392022-chr11:62621970..62625527,4	K562	blood:
15	chr11:62357691..62360390-chr11:62623455..62624975,2	MCF-7	breast:
16	chr11:62492410..62497148-chr11:62620379..62625675,11	K562	blood:
17	chr11:62473688..62475805-chr11:62622758..62625720,5	K562	blood:
18	chr11:62431862..62434344-chr11:62623258..62625462,3	K562	blood:
19	chr11:62365338..62373022-chr11:62621930..62625872,13	K562	blood:
20	chr11:62365951..62369565-chr11:62622521..62625872,5	K562	blood:
21	chr11:62476521..62478365-chr11:62623672..62625247,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNHG1	TF binding region
ENSG00000214753	Chromatin interaction
ENSG00000162188	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000269463	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000149499	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000149480	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000168569	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000149016	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11231220	1.00[AMR][1000 genomes]
rs11231261	0.91[AFR][1000 genomes]
rs12270342	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12288417	1.00[AMR][1000 genomes]
rs12290152	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12292281	1.00[AMR][1000 genomes]
rs12295052	1.00[AMR][1000 genomes]
rs28400288	1.00[AMR][1000 genomes]
rs56994557	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58003814	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58505493	1.00[AMR][1000 genomes]
rs58792209	1.00[AMR][1000 genomes]
rs59143369	1.00[AMR][1000 genomes]
rs61088491	1.00[AMR][1000 genomes]
rs73483955	1.00[AMR][1000 genomes]
rs73483965	1.00[AMR][1000 genomes]
rs73483978	1.00[AMR][1000 genomes]
rs73485621	1.00[AMR][1000 genomes]
rs73485634	1.00[AMR][1000 genomes]
rs73485689	1.00[AMR][1000 genomes]
rs73487820	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487823	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487824	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487852	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73502144	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong 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	1401 gene(s)	inside rSNPs	diseases
4	nsv508636	chr11:62547114-62644458	Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1195 gene(s)	inside rSNPs	diseases
5	nsv1051308	chr11:62564713-62673136	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
6	nsv541058	chr11:62564713-62673136	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
7	nsv1041770	chr11:62610353-62871767	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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 target site	263 gene(s)	inside rSNPs	diseases
8	nsv983154	chr11:62621265-62625410	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	133 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62620600-62626000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:62620800-62626000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:62622200-62625000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr11:62622400-62625600	Active TSS	GM12878-XiMat	blood
5	chr11:62622600-62625200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:62622800-62625000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:62622800-62625600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr11:62622800-62625600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:62623000-62625200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:62623000-62625200	Active TSS	Hela-S3	cervix
11	chr11:62623000-62625400	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr11:62623000-62626000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:62623000-62626400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr11:62623000-62626400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr11:62623000-62626600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:62623000-62627000	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr11:62623200-62625000	Active TSS	K562	blood
18	chr11:62623200-62625200	Active TSS	A549	lung
19	chr11:62623200-62625600	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr11:62623200-62625800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr11:62623200-62626400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:62623200-62626400	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr11:62623200-62627000	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr11:62623600-62625000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:62623600-62625400	Flanking Active TSS	Fetal Thymus	thymus
26	chr11:62624000-62625000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:62624000-62625000	Active TSS	HepG2	liver
28	chr11:62624000-62625400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:62624000-62625800	Enhancers	Spleen	Spleen
30	chr11:62624200-62625000	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr11:62624200-62625000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:62624200-62625000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr11:62624200-62625000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:62624200-62625000	Enhancers	Right Ventricle	heart
35	chr11:62624200-62625200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr11:62624200-62625200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr11:62624200-62625200	Weak transcription	Stomach Mucosa	stomach
38	chr11:62624200-62625400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr11:62624200-62625400	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr11:62624200-62625400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:62624200-62625800	Active TSS	Brain Angular Gyrus	brain
42	chr11:62624200-62625800	Enhancers	Fetal Heart	heart
43	chr11:62624200-62626000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr11:62624200-62627000	Weak transcription	Gastric	stomach
45	chr11:62624200-62630600	Weak transcription	HSMMtube	muscle
46	chr11:62624200-62646800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr11:62624400-62625000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr11:62624400-62625000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr11:62624400-62625000	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr11:62624400-62625200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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