Variant report

Variant	rs2380117
Chromosome Location	chr1:247359800-247359801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247357951..247361056-chr1:247361923..247364396,3	MCF-7	breast:
2	chr1:247357229..247359962-chr1:247372400..247373905,2	K562	blood:
3	chr1:247358659..247361289-chr1:247379963..247382060,2	K562	blood:
4	chr1:247353227..247354818-chr1:247357854..247360408,2	K562	blood:
5	chr1:247357112..247360279-chr1:247371102..247373822,3	MCF-7	breast:
6	chr1:247357131..247359962-chr1:247372294..247374623,3	K562	blood:
7	chr1:247351089..247353173-chr1:247358781..247361501,2	K562	blood:
8	chr1:247357137..247358691-chr1:247359403..247361860,2	K562	blood:
9	chr1:247341025..247343921-chr1:247358024..247360237,2	K562	blood:
10	chr1:247239136..247240695-chr1:247358681..247361608,2	K562	blood:
11	chr1:247351089..247356091-chr1:247358781..247361501,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259865	Chromatin interaction
ENSG00000227671	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10924964	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1115202	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567626	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12569042	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17269923	0.98[EUR][1000 genomes]
rs2892054	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35229190	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3738443	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41315860	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4269806	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4351686	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551629	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4582838	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55643126	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55675011	0.91[AFR][1000 genomes]
rs55914345	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56029850	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56046175	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56065612	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56340510	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57178323	0.93[AFR][1000 genomes]
rs58405512	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60240280	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60698393	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61839991	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61839994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839997	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61840000	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61840048	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61840053	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61840054	0.89[EUR][1000 genomes]
rs61840055	0.86[EUR][1000 genomes]
rs61840056	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61840057	0.89[EUR][1000 genomes]
rs61840059	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6656425	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660351	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6665647	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666543	0.89[EUR][1000 genomes]
rs6668154	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680197	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6684181	0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6698690	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74152976	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74152980	0.90[AFR][1000 genomes]
rs74152988	0.85[AFR][1000 genomes]
rs7536883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546908	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7551871	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
7	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1012616	chr1:247173851-247365588	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv535420	chr1:247173851-247365588	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
12	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
13	nsv873433	chr1:247278707-247360368	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
14	nsv873434	chr1:247319489-247360368	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
15	nsv873435	chr1:247336726-247360368	Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
16	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a
17	nsv873437	chr1:247340784-247366380	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	n/a
18	nsv873438	chr1:247347971-247366380	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2380117	RP11-488L18.10	cis	lung	GTEx
rs2380117	RP11-488L18.10	cis	Artery Tibial	GTEx
rs2380117	RP11-488L18.10	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:131 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247346000-247370200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:247346000-247371800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr1:247347400-247362000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:247349600-247361000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:247351400-247360000	ZNF genes & repeats	Dnd41	blood
6	chr1:247351800-247372400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr1:247352000-247368200	ZNF genes & repeats	Liver	Liver
8	chr1:247353000-247361800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr1:247353000-247362200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:247353000-247367200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:247353000-247368000	ZNF genes & repeats	Primary B cells from cord blood	blood
12	chr1:247353000-247370400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:247353200-247359800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
14	chr1:247353200-247360200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:247353400-247359800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
16	chr1:247353400-247372000	ZNF genes & repeats	GM12878-XiMat	blood
17	chr1:247353600-247360600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:247353800-247362200	Weak transcription	Hela-S3	cervix
19	chr1:247354000-247371000	Weak transcription	Brain Angular Gyrus	brain
20	chr1:247354800-247360000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:247354800-247360200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:247354800-247371200	Weak transcription	Stomach Mucosa	stomach
23	chr1:247354800-247372400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:247354800-247372400	Weak transcription	Right Ventricle	heart
25	chr1:247355000-247362400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:247356000-247359800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:247356000-247359800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:247356000-247359800	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:247356000-247360400	Weak transcription	HSMMtube	muscle
30	chr1:247356000-247361200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:247356000-247361400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:247356000-247361600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:247356000-247362000	Weak transcription	HepG2	liver
34	chr1:247356000-247362400	Weak transcription	Pancreas	Pancrea
35	chr1:247356000-247363400	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr1:247356000-247367200	Weak transcription	Brain Substantia Nigra	brain
37	chr1:247356000-247367800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:247356000-247372400	Weak transcription	Brain Anterior Caudate	brain
39	chr1:247356000-247372400	Weak transcription	Fetal Brain Male	brain
40	chr1:247356000-247372600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:247356000-247372600	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:247356200-247360400	Weak transcription	NHLF	lung
43	chr1:247356200-247372400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:247356200-247372400	Weak transcription	Colonic Mucosa	Colon
45	chr1:247356400-247361600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:247356400-247364600	Weak transcription	Aorta	Aorta
47	chr1:247356400-247372400	Weak transcription	Gastric	stomach
48	chr1:247356600-247364400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:247356600-247367800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:247357000-247367400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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