Variant report

Variant	rs17475753
Chromosome Location	chr1:223002704-223002705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:223002580-223002730	A549	lung:	n/a	n/a
2	CTCF	chr1:223002620-223002770	HVMF	connective:	n/a	n/a
3	CTCF	chr1:223002580-223002730	GM12864	blood:	n/a	n/a
4	CTCF	chr1:223002640-223002790	NHDF-neo	bronchial:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:222998480..223000211-chr1:223000918..223003363,2	MCF-7	breast:
2	chr1:222986827..222988630-chr1:223000881..223002859,2	MCF-7	breast:
3	chr1:223001258..223003363-chr1:223007467..223009599,2	MCF-7	breast:
4	chr1:222986729..222989819-chr1:223001002..223005734,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228106	TF binding region
ENSG00000154309	Chromatin interaction
ENSG00000228106	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10495202	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132369	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1132371	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11588378	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12734196	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17475431	0.94[EUR][1000 genomes]
rs17475774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17477752	0.86[AMR][1000 genomes]
rs17534704	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17534774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17535032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17535137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17536056	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17536209	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17536299	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17536396	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17536522	0.86[AMR][1000 genomes]
rs34080450	0.82[AMR][1000 genomes]
rs34096996	0.93[EUR][1000 genomes]
rs34139393	0.93[EUR][1000 genomes]
rs34151467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34194482	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34225287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34229647	0.95[EUR][1000 genomes]
rs34232799	0.82[AMR][1000 genomes]
rs34277924	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34299243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34300028	0.92[EUR][1000 genomes]
rs34355153	0.86[AMR][1000 genomes]
rs34503525	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs34505570	0.94[EUR][1000 genomes]
rs34643369	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34651530	0.82[EUR][1000 genomes]
rs34690779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34701716	0.82[AMR][1000 genomes]
rs34713681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34755094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34761499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34774807	0.86[AMR][1000 genomes]
rs34791822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34804073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34893395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34898792	0.93[EUR][1000 genomes]
rs34950986	0.94[EUR][1000 genomes]
rs34962524	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35131473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35197173	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35217299	0.82[AMR][1000 genomes]
rs35270311	0.96[EUR][1000 genomes]
rs35270996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35283922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35319605	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35356885	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35399857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497286	0.94[EUR][1000 genomes]
rs35506390	0.86[AMR][1000 genomes]
rs35538644	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs35578837	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35591569	0.93[EUR][1000 genomes]
rs35597626	0.86[AMR][1000 genomes]
rs35597790	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35689138	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs35756512	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35773347	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35787799	0.93[EUR][1000 genomes]
rs35898924	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35912520	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35947021	0.82[AMR][1000 genomes]
rs36032255	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36066427	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36090356	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36113407	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4298738	0.86[AMR][1000 genomes]
rs61838099	0.87[EUR][1000 genomes]
rs61838105	0.94[EUR][1000 genomes]
rs61838107	0.93[EUR][1000 genomes]
rs61838113	0.96[EUR][1000 genomes]
rs61838115	0.96[EUR][1000 genomes]
rs61838118	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839587	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839588	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839589	1.00[ASN][1000 genomes]
rs61839600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61839601	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61839602	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61840263	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61840271	0.86[AMR][1000 genomes]
rs61840273	0.86[AMR][1000 genomes]
rs71644708	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71644709	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71644714	0.86[AMR][1000 genomes]
rs71644716	0.91[AMR][1000 genomes]
rs71644718	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	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
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222989400-223002800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:222989400-223026800	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:222990400-223027400	Weak transcription	Primary B cells from cord blood	blood
4	chr1:222991200-223010200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:222991800-223003200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:222991800-223017200	Weak transcription	Aorta	Aorta
7	chr1:222994000-223003200	Weak transcription	Osteobl	bone
8	chr1:222994600-223003400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:222994800-223003200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:222995200-223003400	Weak transcription	NHDF-Ad	bronchial
11	chr1:222995800-223003200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:222997000-223016600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:222998200-223003200	Weak transcription	A549	lung
14	chr1:222998200-223003600	Weak transcription	Ovary	ovary
15	chr1:222998400-223006600	Weak transcription	Fetal Lung	lung
16	chr1:222998600-223003400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:222999400-223003200	Weak transcription	Stomach Mucosa	stomach
18	chr1:222999600-223002800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:222999600-223015600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:223001200-223002800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr1:223001200-223003400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:223001400-223003400	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr1:223001800-223003800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr1:223001800-223004000	Enhancers	Colon Smooth Muscle	Colon
25	chr1:223001800-223012000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:223001800-223012200	Weak transcription	Hela-S3	cervix
27	chr1:223002000-223002800	Weak transcription	Brain Substantia Nigra	brain
28	chr1:223002200-223017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:223002400-223004000	Enhancers	Rectal Smooth Muscle	rectum
30	chr1:223002600-223003600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:223002600-223003800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:223002600-223003800	Enhancers	HepG2	liver
33	chr1:223002600-223019800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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