Variant report

Variant	rs1640820
Chromosome Location	chr1:223314508-223314509
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:223314500-223314650	AG09319	gingival:	n/a	n/a
2	FOXA1	chr1:223314329-223314716	T-47D	breast:	n/a	n/a
3	CTCF	chr1:223314480-223314630	HMEC	breast:	n/a	n/a
4	CTCF	chr1:223314500-223314650	HAc	cerebellar:	n/a	n/a
5	STAT3	chr1:223314194-223314560	MCF10A-Er-Src	breast:	n/a	n/a
6	USF2	chr1:223314471-223314528	GM12878	blood:	n/a	n/a
7	CTCF	chr1:223314500-223314650	HEEpiC	esophagus:	n/a	n/a
8	CTCF	chr1:223314480-223314630	SAEC	small airway:	n/a	n/a
9	CTCF	chr1:223314500-223314650	AG10803	skin:	n/a	n/a
10	CTCF	chr1:223314500-223314650	NHDF-neo	bronchial:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223305699..223307476-chr1:223314416..223316383,2	K562	blood:
2	chr1:223308071..223311101-chr1:223314181..223317156,4	K562	blood:
3	chr1:223314112..223315763-chr1:223428668..223430244,2	MCF-7	breast:
4	chr1:223309835..223312758-chr1:223314072..223315827,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236846	TF binding region
TLR5	TF binding region
ENSG00000187554	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10489492	0.95[ASN][1000 genomes]
rs11485986	1.00[AMR][1000 genomes]
rs11486079	0.91[ASN][1000 genomes]
rs1361642	0.98[ASN][1000 genomes]
rs1418145	0.89[ASN][1000 genomes]
rs1418146	0.89[ASN][1000 genomes]
rs1612398	0.91[ASN][1000 genomes]
rs1640803	0.93[ASN][1000 genomes]
rs1640809	0.95[ASN][1000 genomes]
rs1640811	0.95[ASN][1000 genomes]
rs1640812	0.95[ASN][1000 genomes]
rs1640813	0.95[ASN][1000 genomes]
rs1640814	0.95[ASN][1000 genomes]
rs1640815	0.95[ASN][1000 genomes]
rs1640816	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1640817	0.98[ASN][1000 genomes]
rs1640818	0.98[ASN][1000 genomes]
rs1640819	0.98[ASN][1000 genomes]
rs1640822	0.93[AFR][1000 genomes]
rs1640823	0.98[ASN][1000 genomes]
rs17163743	0.91[ASN][1000 genomes]
rs1773738	0.95[ASN][1000 genomes]
rs1773744	0.95[ASN][1000 genomes]
rs1773749	0.91[ASN][1000 genomes]
rs1773753	0.93[ASN][1000 genomes]
rs1773754	0.91[ASN][1000 genomes]
rs1773761	0.95[ASN][1000 genomes]
rs1773762	0.95[ASN][1000 genomes]
rs1773763	0.95[ASN][1000 genomes]
rs1773765	0.95[ASN][1000 genomes]
rs1773766	0.98[ASN][1000 genomes]
rs1773767	0.98[ASN][1000 genomes]
rs1773768	0.98[ASN][1000 genomes]
rs1935305	0.95[ASN][1000 genomes]
rs2241095	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2256707	0.95[ASN][1000 genomes]
rs2302597	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2353474	0.93[ASN][1000 genomes]
rs2430400	0.95[ASN][1000 genomes]
rs2487834	0.95[ASN][1000 genomes]
rs2487836	0.95[ASN][1000 genomes]
rs34136554	0.95[ASN][1000 genomes]
rs34552707	0.91[ASN][1000 genomes]
rs35579200	0.91[ASN][1000 genomes]
rs45501199	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs5744135	0.86[ASN][1000 genomes]
rs5744138	0.86[ASN][1000 genomes]
rs5744139	0.86[ASN][1000 genomes]
rs5744140	0.86[ASN][1000 genomes]
rs5744143	0.86[ASN][1000 genomes]
rs5744145	0.86[ASN][1000 genomes]
rs5744147	0.86[ASN][1000 genomes]
rs5744149	0.86[ASN][1000 genomes]
rs66553000	0.91[ASN][1000 genomes]
rs66662427	0.95[ASN][1000 genomes]
rs66757010	0.95[ASN][1000 genomes]
rs66832195	0.95[ASN][1000 genomes]
rs66938974	0.91[ASN][1000 genomes]
rs67573944	0.95[ASN][1000 genomes]
rs67623966	0.91[ASN][1000 genomes]
rs67639934	0.91[ASN][1000 genomes]
rs67883821	0.91[ASN][1000 genomes]
rs723961	0.95[ASN][1000 genomes]
rs72743851	0.95[ASN][1000 genomes]
rs72743852	0.93[ASN][1000 genomes]
rs73118159	0.91[ASN][1000 genomes]
rs73118168	0.93[ASN][1000 genomes]
rs759303	0.95[ASN][1000 genomes]
rs763389	0.84[ASN][1000 genomes]
rs988241	0.91[ASN][1000 genomes]
rs988242	0.91[ASN][1000 genomes]
rs988779	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223303200-223314600	Weak transcription	Spleen	Spleen
2	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
3	chr1:223308800-223314600	Weak transcription	Colonic Mucosa	Colon
4	chr1:223309200-223315800	Weak transcription	Primary T cells from cord blood	blood
5	chr1:223309400-223316000	Weak transcription	NHLF	lung
6	chr1:223309600-223314600	Weak transcription	Ovary	ovary
7	chr1:223309600-223314600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:223309800-223315600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:223310200-223316000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:223310600-223315400	Weak transcription	Lung	lung
11	chr1:223311200-223314600	Weak transcription	Stomach Mucosa	stomach
12	chr1:223311200-223315800	Weak transcription	Hela-S3	cervix
13	chr1:223311200-223316000	Weak transcription	Liver	Liver
14	chr1:223311400-223316000	Weak transcription	Fetal Intestine Large	intestine
15	chr1:223311600-223315600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:223311600-223316000	Weak transcription	Fetal Intestine Small	intestine
17	chr1:223311600-223316200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:223312600-223315000	Genic enhancers	Monocytes-CD14+_RO01746	blood
19	chr1:223313400-223315600	Enhancers	Fetal Muscle Leg	muscle
20	chr1:223313600-223315800	Enhancers	Fetal Muscle Trunk	muscle
21	chr1:223313800-223314600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:223313800-223315000	Enhancers	Fetal Thymus	thymus
23	chr1:223313800-223315800	Enhancers	Placenta	Placenta
24	chr1:223314000-223314600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:223314000-223314600	Enhancers	Adipose Nuclei	Adipose
26	chr1:223314000-223314600	Enhancers	Brain Anterior Caudate	brain
27	chr1:223314000-223314800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:223314000-223314800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:223314000-223314800	Enhancers	Fetal Lung	lung
30	chr1:223314000-223314800	Enhancers	Fetal Stomach	stomach
31	chr1:223314000-223315000	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
32	chr1:223314000-223315400	Enhancers	Primary B cells from cord blood	blood
33	chr1:223314000-223315600	Enhancers	Gastric	stomach
34	chr1:223314000-223315800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:223314000-223315800	Enhancers	Esophagus	oesophagus
36	chr1:223314000-223315800	Enhancers	Pancreas	Pancrea
37	chr1:223314000-223316000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:223314200-223314600	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:223314200-223314800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
40	chr1:223314200-223314800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
41	chr1:223314200-223314800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
42	chr1:223314200-223314800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
43	chr1:223314200-223314800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
44	chr1:223314200-223314800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:223314200-223314800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:223314200-223314800	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr1:223314200-223314800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:223314200-223314800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:223314200-223314800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr1:223314200-223314800	Enhancers	NH-A	brain

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