Variant report

Variant	rs6688800
Chromosome Location	chr1:153599390-153599391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:126)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:126 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr1:153599292-153600415	MCF-7	breast:	n/a	n/a
2	TCF12	chr1:153599182-153600464	A549	lung:	n/a	n/a
3	EGR1	chr1:153599274-153599771	ECC-1	luminal epithelium:	n/a	chr1:153599488-153599502
4	ZNF384	chr1:153599385-153600472	K562	blood:	n/a	n/a
5	ZBTB7A	chr1:153599183-153600573	ECC-1	luminal epithelium:	n/a	chr1:153600154-153600163
6	POLR2A	chr1:153599381-153600254	K562	blood:	n/a	n/a
7	POLR2A	chr1:153599307-153600336	ProgFib	skin:	n/a	n/a
8	TAF1	chr1:153599322-153599747	K562	blood:	n/a	n/a
9	MAX	chr1:153599302-153600381	ECC-1	luminal epithelium:	n/a	n/a
10	SRF	chr1:153599260-153600305	MCF-7	breast:	n/a	n/a
11	MAX	chr1:153599353-153600326	K562	blood:	n/a	n/a
12	POLR2A	chr1:153599058-153600390	HUVEC	blood vessel:	n/a	n/a
13	RCOR1	chr1:153599368-153600400	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:153599325-153600199	K562	blood:	n/a	n/a
15	MYC	chr1:153599315-153600298	K562	blood:	n/a	n/a
16	POLR2A	chr1:153598964-153600383	K562	blood:	n/a	n/a
17	MYC	chr1:153599383-153600316	Hela-S3	cervix:	n/a	n/a
18	KAP1	chr1:153599368-153600341	U2OS	brain:	n/a	n/a
19	POLR2A	chr1:153599156-153600167	HUVEC	blood vessel:	n/a	n/a
20	RFX5	chr1:153599384-153600331	Hela-S3	cervix:	n/a	chr1:153600304-153600313
21	POLR2A	chr1:153598701-153600412	PFSK-1	brain:	n/a	n/a
22	ELK1	chr1:153599186-153600233	Hela-S3	cervix:	n/a	n/a
23	NR2F2	chr1:153598686-153600424	MCF-7	breast:	n/a	n/a
24	RUNX3	chr1:153599299-153599636	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:153598773-153600354	K562	blood:	n/a	n/a
26	POLR2A	chr1:153599253-153600343	K562	blood:	n/a	n/a
27	POLR2A	chr1:153599329-153600349	MCF-7	breast:	n/a	n/a
28	HEY1	chr1:153599357-153600235	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:153599299-153600201	U87	brain:	n/a	n/a
30	YY1	chr1:153599384-153599651	K562	blood:	n/a	n/a
31	POLR2A	chr1:153599320-153600189	K562	blood:	n/a	n/a
32	ZMIZ1	chr1:153599324-153600313	K562	blood:	n/a	n/a
33	POLR2A	chr1:153599152-153600280	Hela-S3	cervix:	n/a	n/a
34	SMARCC1	chr1:153598771-153600492	Hela-S3	cervix:	n/a	n/a
35	NR2F2	chr1:153599229-153600860	K562	blood:	n/a	n/a
36	POLR2A	chr1:153599352-153599633	HUVEC	blood vessel:	n/a	n/a
37	TBP	chr1:153599324-153600259	K562	blood:	n/a	n/a
38	POLR2A	chr1:153598479-153600409	HepG2	liver:	n/a	n/a
39	CTCF	chr1:153599255-153600894	A549	lung:	n/a	n/a
40	POLR2A	chr1:153599346-153600306	HCT-116	colon:	n/a	n/a
41	MAX	chr1:153599040-153600279	Hela-S3	cervix:	n/a	n/a
42	KAP1	chr1:153599385-153600405	HEK293	kidney:	n/a	n/a
43	TCF12	chr1:153599185-153600362	ECC-1	luminal epithelium:	n/a	n/a
44	NR2F2	chr1:153599150-153600279	MCF-7	breast:	n/a	n/a
45	TBL1XR1	chr1:153599359-153600310	K562	blood:	n/a	n/a
46	HEY1	chr1:153599349-153600164	K562	blood:	n/a	n/a
47	MAX	chr1:153599337-153600311	NB4	blood:	n/a	n/a
48	POLR2A	chr1:153599368-153600209	NB4	blood:	n/a	n/a
49	POLR2A	chr1:153598765-153600521	MCF10A-Er-Src	breast:	n/a	n/a
50	TCF12	chr1:153599341-153600380	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153599385..153600186-chr6:26285196..26286148,2	Hela-S3	cervix:
2	chr1:153599062..153600037-chr19:1275773..1276281,2	Hela-S3	cervix:
3	chr1:153599100..153600094-chr14:102829264..102829864,2	Hela-S3	cervix:
4	chr1:153599294..153600058-chr12:3068523..3069080,2	Hela-S3	cervix:
5	chr1:153598961..153599821-chr7:6048148..6049140,2	Hela-S3	cervix:
6	chr1:153505870..153508233-chr1:153598440..153600666,2	MCF-7	breast:
7	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
8	chr1:153598208..153601029-chr1:153962097..153964477,2	K562	blood:
9	chr1:153598961..153599471-chr11:65189962..65190917,2	Hela-S3	cervix:
10	chr1:153599101..153601090-chr1:153642486..153644716,4	MCF-7	breast:
11	chr1:153515275..153518447-chr1:153598676..153601896,4	MCF-7	breast:
12	chr1:153517525..153519027-chr1:153598182..153599900,2	K562	blood:
13	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
14	chr1:153597855..153601076-chr1:153629883..153633781,4	MCF-7	breast:
15	chr1:153598241..153600189-chr1:153949006..153951530,2	MCF-7	breast:
16	chr1:153537634..153542525-chr1:153598837..153602183,9	K562	blood:
17	chr1:153599321..153600251-chr9:134269301..134270091,2	Hela-S3	cervix:
18	chr1:153599154..153601344-chr1:153747056..153749212,2	MCF-7	breast:
19	chr1:153599062..153600033-chr7:32982293..32983190,2	Hela-S3	cervix:
20	chr1:153538054..153540599-chr1:153598556..153600339,3	K562	blood:
21	chr1:153598392..153603036-chr1:153933813..153937554,5	MCF-7	breast:

No data

Variant related genes	Relation type
S100A1	TF binding region
ENSG00000143553	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000228300	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143543	Chromatin interaction
ENSG00000106305	Chromatin interaction
ENSG00000205763	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000272654	Chromatin interaction
ENSG00000196663	Chromatin interaction
ENSG00000130723	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000197905	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000158406	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11805092	1.00[AMR][1000 genomes]
rs13305995	0.85[AMR][1000 genomes]
rs13305998	1.00[AMR][1000 genomes]
rs13306004	0.85[AMR][1000 genomes]
rs73009954	1.00[ASN][1000 genomes]
rs73011760	1.00[AMR][1000 genomes]
rs7516222	0.85[AMR][1000 genomes]
rs9660389	1.00[ASN][1000 genomes]
rs9660416	1.00[ASN][1000 genomes]
rs9728400	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153589200-153599400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:153590600-153599400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:153596800-153600400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:153597600-153600600	Enhancers	GM12878-XiMat	blood
5	chr1:153597800-153600800	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr1:153598200-153603600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr1:153598400-153599400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:153598400-153599600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:153598400-153599600	Flanking Active TSS	Hela-S3	cervix
10	chr1:153598400-153600200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:153598400-153600200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr1:153598400-153600400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:153598400-153600400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:153598600-153599400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:153598600-153599400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:153598600-153599400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:153598600-153599400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:153598600-153599400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:153598600-153599400	Flanking Active TSS	Brain Substantia Nigra	brain
20	chr1:153598600-153599400	Enhancers	Gastric	stomach
21	chr1:153598600-153599600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:153598600-153599600	Enhancers	Spleen	Spleen
23	chr1:153598600-153599600	Flanking Active TSS	NH-A	brain
24	chr1:153598600-153599800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr1:153598600-153600200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:153598600-153600400	Flanking Active TSS	Colonic Mucosa	Colon
27	chr1:153598600-153600400	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr1:153598600-153600400	Flanking Active TSS	HUVEC	blood vessel
29	chr1:153598600-153601800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr1:153598800-153599400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:153598800-153599400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:153598800-153599400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:153598800-153599400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr1:153598800-153599400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:153598800-153599400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr1:153598800-153599400	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr1:153598800-153599400	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr1:153598800-153599400	Flanking Active TSS	Left Ventricle	heart
39	chr1:153598800-153599400	Flanking Active TSS	Right Atrium	heart
40	chr1:153598800-153599400	Flanking Active TSS	A549	lung
41	chr1:153598800-153599600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr1:153598800-153599600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:153598800-153599600	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr1:153598800-153599600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:153598800-153599600	Flanking Active TSS	HepG2	liver
46	chr1:153598800-153599600	Flanking Active TSS	HSMMtube	muscle
47	chr1:153598800-153599800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:153598800-153600000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:153598800-153600000	Flanking Active TSS	Liver	Liver
50	chr1:153598800-153600000	Flanking Active TSS	Fetal Heart	heart

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