Variant report

Variant	rs867677
Chromosome Location	chr4:79513607-79513608
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:79513571-79513917	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:79513417-79513978	MCF10A-Er-Src	breast:	n/a	n/a
3	TBL1XR1	chr4:79513363-79513856	GM12878	blood:	n/a	n/a
4	RAD21	chr4:79513472-79514156	GM12878	blood:	n/a	n/a
5	CTCF	chr4:79513574-79513888	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr4:79513565-79513893	HepG2	liver:	n/a	n/a
7	RAD21	chr4:79513551-79513895	H1-hESC	embryonic stem cell:	n/a	n/a
8	EBF1	chr4:79513261-79513768	GM12878	blood:	n/a	n/a
9	CTCF	chr4:79513560-79513710	AG09319	gingival:	n/a	n/a
10	RAD21	chr4:79513603-79513817	HepG2	liver:	n/a	n/a
11	CTCF	chr4:79513600-79513750	HVMF	connective:	n/a	n/a
12	CTCF	chr4:79513553-79513927	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr4:79513540-79513690	A549	lung:	n/a	n/a
14	CTCF	chr4:79513607-79513821	HUVEC	blood vessel:	n/a	n/a
15	STAT3	chr4:79513290-79514193	GM12878	blood:	n/a	chr4:79514070-79514081
16	EP300	chr4:79513218-79513834	GM12878	blood:	n/a	chr4:79513246-79513260
17	CTCF	chr4:79513540-79513690	NHDF-neo	bronchial:	n/a	n/a
18	CTCF	chr4:79513580-79513730	RPTEC	kidney:	n/a	n/a
19	ZNF143	chr4:79513568-79513886	GM12878	blood:	n/a	n/a
20	RCOR1	chr4:79513207-79513830	GM12878	blood:	n/a	n/a
21	CTCF	chr4:79513581-79513771	A549	lung:	n/a	n/a
22	RCOR1	chr4:79513569-79513742	K562	blood:	n/a	n/a
23	CTCF	chr4:79513600-79513750	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr4:79513578-79513849	GM12878	blood:	n/a	n/a
25	CTCF	chr4:79513520-79513670	HMEC	breast:	n/a	n/a
26	MXI1	chr4:79513262-79514041	GM12878	blood:	n/a	n/a
27	CTCF	chr4:79513605-79513814	SK-N-SH_RA	brain:	n/a	n/a
28	CTCF	chr4:79513500-79513650	HAc	cerebellar:	n/a	n/a
29	SMC3	chr4:79513602-79513883	K562	blood:	n/a	n/a
30	CTCF	chr4:79513540-79513690	HCM	heart:	n/a	n/a
31	CTCF	chr4:79513560-79513710	HFF-Myc	foreskin:	n/a	n/a
32	EP300	chr4:79512935-79513812	GM12878	blood:	n/a	chr4:79513246-79513260
33	PBX3	chr4:79513413-79513641	GM12878	blood:	n/a	n/a
34	CTCF	chr4:79513600-79513841	K562	blood:	n/a	n/a
35	CTCF	chr4:79513578-79513968	K562	blood:	n/a	n/a
36	CTCF	chr4:79513600-79513750	GM12871	blood:	n/a	n/a
37	CTCF	chr4:79513518-79514126	K562	blood:	n/a	n/a
38	EP300	chr4:79512928-79513813	GM12878	blood:	n/a	chr4:79513246-79513260
39	CTCF	chr4:79513580-79513730	AoAF	blood vessel:	n/a	n/a
40	RAD21	chr4:79513584-79513794	GM12878	blood:	n/a	n/a
41	CTCF	chr4:79513470-79513992	GM12878	blood:	n/a	n/a
42	RAD21	chr4:79513564-79513815	SK-N-SH_RA	brain:	n/a	n/a
43	CTCF	chr4:79513540-79513690	HVMF	connective:	n/a	n/a
44	CTCF	chr4:79513580-79513730	HL-60	blood:	n/a	n/a
45	RAD21	chr4:79513484-79513955	HCT-116	colon:	n/a	n/a
46	CTCF	chr4:79513554-79513980	K562	blood:	n/a	n/a
47	CTCF	chr4:79513580-79513730	HA-sp	spinal cord:	n/a	n/a
48	RAD21	chr4:79513555-79513946	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr4:79513600-79513750	HA-sp	spinal cord:	n/a	n/a
50	RCOR1	chr4:79513549-79513832	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79509559..79512008-chr4:79512168..79514182,2	K562	blood:
2	chr4:79513272..79514062-chr4:79785483..79786626,3	K562	blood:

No data

Variant related genes	Relation type
ANXA3	TF binding region

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10003947	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11098257	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12509033	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12641838	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12642521	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13126934	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1472365	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1587222	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1587223	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1874486	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1874487	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1874488	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1995062	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2867462	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805174	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3805175	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4466067	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975147	1.00[CHB][hapmap]
rs6533804	0.95[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833514	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6851992	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7654600	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7656476	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7679218	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7682502	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7683399	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7683582	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9307409	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs950699	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active 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	41 gene(s)	inside rSNPs	diseases
2	nsv967949	chr4:79511515-79527707	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79474400-79527200	Weak transcription	Spleen	Spleen
2	chr4:79481800-79521000	Weak transcription	Right Ventricle	heart
3	chr4:79483000-79530000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:79488400-79523600	Weak transcription	Esophagus	oesophagus
5	chr4:79488400-79527400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:79490000-79523400	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:79490600-79521000	Weak transcription	Fetal Heart	heart
8	chr4:79490800-79532600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:79491000-79529600	Weak transcription	Aorta	Aorta
10	chr4:79491200-79535400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:79491800-79533200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:79491800-79542600	Weak transcription	NH-A	brain
13	chr4:79492000-79531600	Strong transcription	HMEC	breast
14	chr4:79500000-79522200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:79501400-79516000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:79502200-79529200	Weak transcription	Colonic Mucosa	Colon
17	chr4:79502400-79525800	Weak transcription	Psoas Muscle	Psoas
18	chr4:79502400-79532200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr4:79503200-79521800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:79505800-79517200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:79506400-79517200	Weak transcription	Pancreas	Pancrea
22	chr4:79506400-79517200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:79506800-79523800	Weak transcription	Placenta	Placenta
24	chr4:79507600-79521000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:79508200-79533600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:79508600-79523600	Weak transcription	Adipose Nuclei	Adipose
27	chr4:79508800-79525400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:79508800-79527000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:79508800-79527400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:79509600-79515200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:79510000-79517200	Weak transcription	Fetal Stomach	stomach
32	chr4:79510000-79518800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:79510000-79520600	Weak transcription	Lung	lung
34	chr4:79510800-79514200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:79510800-79520800	Weak transcription	Left Ventricle	heart
36	chr4:79510800-79523400	Weak transcription	A549	lung
37	chr4:79511000-79523800	Weak transcription	Hela-S3	cervix
38	chr4:79512000-79513800	Genic enhancers	NHEK	skin
39	chr4:79512400-79523600	Weak transcription	Gastric	stomach
40	chr4:79512400-79524400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:79512600-79534200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:79512600-79536800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:79512800-79525600	Weak transcription	NHLF	lung
44	chr4:79513000-79514000	Enhancers	Stomach Mucosa	stomach
45	chr4:79513200-79514000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:79513200-79514200	Enhancers	GM12878-XiMat	blood
47	chr4:79513400-79513800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:79513400-79513800	Enhancers	Duodenum Mucosa	Duodenum
49	chr4:79513400-79513800	Enhancers	Ovary	ovary
50	chr4:79513400-79513800	Enhancers	Right Atrium	heart

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