Variant report

Variant	rs6591223
Chromosome Location	chr11:66609289-66609290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66608869-66611525	IMR90	lung:	n/a	n/a
2	POLR2A	chr11:66609276-66609332	MCF-7	breast:	n/a	n/a
3	POLR2A	chr11:66608785-66612814	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr11:66609194-66617823	K562	blood:	n/a	n/a
5	POLR2A	chr11:66608768-66611588	GM12892	blood:	n/a	n/a
6	WRNIP1	chr11:66609168-66610278	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:66608824-66610248	K562	blood:	n/a	n/a
8	POLR2A	chr11:66608787-66613638	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:66609278-66609658	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr11:66608551-66610224	HepG2	liver:	n/a	n/a
11	POLR2A	chr11:66608996-66612533	A549	lung:	n/a	n/a
12	POLR2A	chr11:66609275-66611534	HL-60	blood:	n/a	n/a
13	POLR2A	chr11:66609141-66609349	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr11:66608767-66611561	GM12892	blood:	n/a	n/a
15	POLR2A	chr11:66608684-66612061	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:66608942-66611364	GM12891	blood:	n/a	n/a
17	POLR2A	chr11:66608799-66612906	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr11:66608687-66611869	GM12892	blood:	n/a	n/a
19	POLR2A	chr11:66608788-66611382	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:66608790-66609635	GM12891	blood:	n/a	n/a
21	POLR2A	chr11:66609099-66609991	GM12892	blood:	n/a	n/a
22	POLR2A	chr11:66608803-66609362	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr11:66609081-66609613	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:66608006..66612050-chr11:66789663..66791972,5	MCF-7	breast:
2	chr11:66587872..66589833-chr11:66608211..66610611,2	K562	blood:
3	chr11:66607675..66609433-chr11:66725286..66727627,2	MCF-7	breast:
4	chr11:66444643..66447365-chr11:66608477..66611039,2	MCF-7	breast:
5	chr11:66607553..66610979-chr11:66790122..66792121,3	MCF-7	breast:
6	chr11:66608342..66609990-chr11:66741833..66743804,2	K562	blood:
7	chr11:66240024..66242825-chr11:66609200..66612137,2	MCF-7	breast:
8	chr11:66486907..66489706-chr11:66608896..66612610,3	MCF-7	breast:
9	chr11:66457271..66460204-chr11:66608971..66610490,2	MCF-7	breast:
10	chr11:66443889..66447498-chr11:66608460..66612257,3	K562	blood:
11	chr11:66609254..66612019-chr11:66742000..66745352,5	MCF-7	breast:
12	chr11:66607838..66611911-chr11:66724380..66727140,5	MCF-7	breast:

No data

Variant related genes	Relation type
RCE1	TF binding region
ENSG00000173715	Chromatin interaction
ENSG00000173914	Chromatin interaction
ENSG00000173227	Chromatin interaction
ENSG00000173599	Chromatin interaction
ENSG00000174516	Chromatin interaction
ENSG00000255517	Chromatin interaction
ENSG00000173898	Chromatin interaction
ENSG00000173237	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs7122539	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7931485	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9633985	0.82[ASN][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	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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 lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv508638	chr11:66541653-66643634	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
8	nsv897795	chr11:66608521-66637926	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6591223	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs6591223	ACTN3	cis	Muscle Skeletal	GTEx
rs6591223	LRFN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66544000-66609600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:66561600-66609400	Weak transcription	Colonic Mucosa	Colon
3	chr11:66567000-66609800	Weak transcription	Ovary	ovary
4	chr11:66568000-66609400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:66568800-66609600	Weak transcription	Fetal Kidney	kidney
6	chr11:66571000-66609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:66571600-66609600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:66576000-66609600	Weak transcription	Esophagus	oesophagus
9	chr11:66576000-66609800	Weak transcription	Aorta	Aorta
10	chr11:66577000-66609400	Weak transcription	Small Intestine	intestine
11	chr11:66580800-66609600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:66581200-66609800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:66596200-66609600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:66597000-66609600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:66598600-66609600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:66599200-66609600	Weak transcription	Fetal Brain Male	brain
17	chr11:66602000-66609400	Weak transcription	Left Ventricle	heart
18	chr11:66604000-66609400	Weak transcription	Right Ventricle	heart
19	chr11:66604200-66609600	Weak transcription	Brain Substantia Nigra	brain
20	chr11:66605200-66609400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:66606600-66609400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr11:66606600-66609400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr11:66606600-66609600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr11:66606800-66609400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr11:66606800-66609600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr11:66606800-66609600	Enhancers	Brain Anterior Caudate	brain
27	chr11:66607000-66609400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:66607000-66609600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:66607000-66609600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr11:66607200-66609400	Weak transcription	Brain Angular Gyrus	brain
31	chr11:66607200-66609400	Weak transcription	HSMM	muscle
32	chr11:66607200-66609600	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr11:66607600-66609400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:66607600-66609600	Enhancers	Primary B cells from cord blood	blood
35	chr11:66607600-66609600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:66607600-66609800	Enhancers	Pancreas	Pancrea
37	chr11:66607800-66609400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:66607800-66609400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:66607800-66609400	Weak transcription	Spleen	Spleen
40	chr11:66607800-66609400	Genic enhancers	A549	lung
41	chr11:66607800-66609400	Weak transcription	HSMMtube	muscle
42	chr11:66607800-66609600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:66607800-66609600	Genic enhancers	Fetal Thymus	thymus
44	chr11:66607800-66609600	Enhancers	NHLF	lung
45	chr11:66608000-66609400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:66608000-66609400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:66608000-66609400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr11:66608000-66609400	Genic enhancers	NHEK	skin
49	chr11:66608000-66609600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr11:66608000-66609600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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