Variant report

Variant	rs56384325
Chromosome Location	chr1:184728868-184728869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr1:184727974-184728961	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:184722577..184724889-chr1:184727067..184730117,4	MCF-7	breast:
2	chr1:184728189..184730615-chr1:184744000..184745636,2	MCF-7	breast:
3	chr1:184722946..184726170-chr1:184728619..184730766,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf21-7	chr1:184727266-184730133	NONHSAT008399

No data

Variant related genes	Relation type
EDEM3	TF binding region
ENSG00000116406	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10489697	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12067111	0.93[AFR][1000 genomes]
rs12079454	1.00[ASN][1000 genomes]
rs12094196	0.95[AFR][1000 genomes]
rs12096214	0.93[AFR][1000 genomes]
rs16823413	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16823421	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16823429	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2224092	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35779894	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41535944	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55896922	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56741490	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58465130	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs59085958	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59347366	1.00[ASN][1000 genomes]
rs59862212	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61022402	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61823879	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs61823880	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61823882	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61823885	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61823891	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61823908	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6681178	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184724800-184742600	Weak transcription	Gastric	stomach
2	chr1:184725200-184731200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:184725400-184730000	Enhancers	Stomach Mucosa	stomach
4	chr1:184727000-184729000	Weak transcription	Pancreas	Pancrea
5	chr1:184728000-184729600	Enhancers	HepG2	liver
6	chr1:184728200-184729200	Enhancers	HSMM	muscle
7	chr1:184728200-184730000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:184728400-184729000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr1:184728400-184729400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:184728400-184729400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr1:184728400-184729400	Enhancers	A549	lung
12	chr1:184728400-184729600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:184728600-184729200	Enhancers	Fetal Intestine Small	intestine
14	chr1:184728600-184729400	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr1:184728800-184729400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:184728800-184729400	Enhancers	HSMMtube	muscle
17	chr1:184728800-184731200	Weak transcription	Liver	Liver

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