Variant report

Variant	rs6666543
Chromosome Location	chr1:247370197-247370198
allele	C/T
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	POLR2A	chr1:247369350-247370209	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:247370160..247372066-chr1:247376870..247379073,2	MCF-7	breast:
2	chr1:247366973..247371599-chr1:247371697..247375755,6	MCF-7	breast:
3	chr1:247340563..247342412-chr1:247369147..247370920,2	K562	blood:

Variant related genes	Relation type
MIR3916	TF binding region
RNA5SP82	TF binding region
ENSG00000227671	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10924964	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1115202	0.89[EUR][1000 genomes]
rs12567626	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12569042	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17269923	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2380117	0.89[EUR][1000 genomes]
rs2892054	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35229190	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3738443	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41315860	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4269806	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4351686	0.89[EUR][1000 genomes]
rs4551629	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4582838	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55643126	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55914345	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56029850	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56046175	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065612	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56340510	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58405512	0.90[EUR][1000 genomes]
rs60240280	0.86[EUR][1000 genomes]
rs60698393	0.90[EUR][1000 genomes]
rs61839991	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61839994	0.86[EUR][1000 genomes]
rs61839996	0.89[EUR][1000 genomes]
rs61839997	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61840000	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61840048	0.90[EUR][1000 genomes]
rs61840053	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61840054	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61840055	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61840056	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61840057	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61840059	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656425	0.89[EUR][1000 genomes]
rs6660351	0.87[EUR][1000 genomes]
rs6665647	0.87[EUR][1000 genomes]
rs6668154	0.89[EUR][1000 genomes]
rs6680197	0.84[EUR][1000 genomes]
rs6684181	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6698690	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74152976	0.96[EUR][1000 genomes]
rs7536883	0.89[EUR][1000 genomes]
rs7546908	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7551871	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6666543	RP11-488L18.10	cis	Artery Tibial	GTEx
rs6666543	RP11-488L18.10	cis	Adipose Subcutaneous	GTEx
rs6666543	RP11-488L18.10	cis	lung	GTEx

Chromatin state (count:122 , 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	chr1:247351800-247372400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr1:247353000-247370400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:247353400-247372000	ZNF genes & repeats	GM12878-XiMat	blood
6	chr1:247354000-247371000	Weak transcription	Brain Angular Gyrus	brain
7	chr1:247354800-247371200	Weak transcription	Stomach Mucosa	stomach
8	chr1:247354800-247372400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:247354800-247372400	Weak transcription	Right Ventricle	heart
10	chr1:247356000-247372400	Weak transcription	Brain Anterior Caudate	brain
11	chr1:247356000-247372400	Weak transcription	Fetal Brain Male	brain
12	chr1:247356000-247372600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:247356000-247372600	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:247356200-247372400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:247356200-247372400	Weak transcription	Colonic Mucosa	Colon
16	chr1:247356400-247372400	Weak transcription	Gastric	stomach
17	chr1:247357200-247370800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr1:247358400-247372400	Weak transcription	Fetal Heart	heart
19	chr1:247359000-247372600	Weak transcription	Fetal Kidney	kidney
20	chr1:247360600-247370400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:247360600-247372400	Weak transcription	Fetal Lung	lung
22	chr1:247360600-247372400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:247361400-247371400	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:247362400-247373400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:247362600-247371000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:247362600-247371200	Weak transcription	HepG2	liver
27	chr1:247362600-247372400	Weak transcription	Psoas Muscle	Psoas
28	chr1:247362600-247372800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:247362800-247372400	Weak transcription	Pancreas	Pancrea
30	chr1:247363000-247372400	Weak transcription	Ovary	ovary
31	chr1:247363000-247372400	Weak transcription	NH-A	brain
32	chr1:247363200-247372600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:247363400-247370800	Weak transcription	Small Intestine	intestine
34	chr1:247363400-247371400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:247363400-247372400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:247363400-247372400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:247363600-247372200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:247363600-247372400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:247363600-247372400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:247363600-247372400	Weak transcription	Placenta	Placenta
41	chr1:247363600-247372400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:247363600-247372400	Weak transcription	Osteobl	bone
43	chr1:247363600-247372600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:247363600-247372800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:247364000-247372600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:247364400-247371800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
47	chr1:247364400-247372400	Weak transcription	NHDF-Ad	bronchial
48	chr1:247365000-247370800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:247365400-247371200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:247365600-247370200	Strong transcription	Fetal Stomach	stomach

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