Variant report

Variant	rs28989221
Chromosome Location	chr4:144296940-144296941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:144296900-144297050	HRPEpiC	eye:	n/a	n/a
2	RAD21	chr4:144296911-144297086	K562	blood:	n/a	n/a
3	CTCF	chr4:144296900-144297050	GM12865	blood:	n/a	n/a
4	CTCF	chr4:144296920-144297070	GM12870	blood:	n/a	n/a
5	FOXA1	chr4:144296808-144297145	T-47D	breast:	n/a	n/a
6	RAD21	chr4:144296833-144297172	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr4:144296940-144297090	AG09319	gingival:	n/a	n/a
8	CTCF	chr4:144296880-144297030	HRE	kidney:	n/a	n/a
9	CTCF	chr4:144296444-144297219	MCF-7	breast:	n/a	chr4:144296581-144296591 chr4:144296578-144296596 chr4:144296573-144296594 chr4:144296584-144296593 chr4:144296579-144296595
10	CTCF	chr4:144296940-144297090	SK-N-SH_RA	brain:	n/a	n/a
11	CTCF	chr4:144296901-144297137	Kidney_OC	kidney:	n/a	n/a
12	RAD21	chr4:144296904-144297104	A549	lung:	n/a	n/a
13	CTCF	chr4:144296920-144297070	GM12864	blood:	n/a	n/a
14	FOXA1	chr4:144296763-144297182	HepG2	liver:	n/a	n/a
15	RAD21	chr4:144296776-144297314	MCF-7	breast:	n/a	n/a
16	YY1	chr4:144296845-144297192	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr4:144296886-144297124	A549	lung:	n/a	n/a
18	RUNX3	chr4:144296711-144297175	GM12878	blood:	n/a	n/a
19	EBF1	chr4:144296736-144297190	GM12878	blood:	n/a	chr4:144297069-144297080
20	CTCF	chr4:144296940-144297090	GM12873	blood:	n/a	n/a
21	NFIC	chr4:144296674-144297731	GM12878	blood:	n/a	n/a
22	CTCF	chr4:144296940-144297090	GM12865	blood:	n/a	n/a
23	CTCF	chr4:144296881-144297117	GM10266	blood:	n/a	n/a
24	CTCF	chr4:144296887-144297170	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr4:144296866-144297118	MCF-7	breast:	n/a	n/a
26	CTCF	chr4:144296900-144297050	HEK293	kidney:	n/a	n/a
27	CTCF	chr4:144296394-144297285	A549	lung:	n/a	chr4:144296581-144296591 chr4:144296578-144296596 chr4:144296573-144296594 chr4:144296584-144296593 chr4:144296579-144296595
28	CTCF	chr4:144296858-144297141	Gliobla	brain:	n/a	n/a
29	CTCF	chr4:144296920-144297070	HVMF	connective:	n/a	n/a
30	CTCF	chr4:144296940-144297090	GM12872	blood:	n/a	n/a
31	CTCF	chr4:144296940-144297090	GM12869	blood:	n/a	n/a
32	CTCF	chr4:144296900-144297050	AG10803	skin:	n/a	n/a
33	CTCF	chr4:144296862-144297146	GM19238	blood:	n/a	n/a
34	CTCF	chr4:144296860-144297010	GM06990	blood:	n/a	n/a
35	CTCF	chr4:144296900-144297050	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr4:144296847-144297139	GM19239	blood:	n/a	n/a
37	CTCF	chr4:144296920-144297070	WERI-Rb-1	eye:	n/a	n/a
38	CTCF	chr4:144296884-144297137	MCF-7	breast:	n/a	n/a
39	CTCF	chr4:144296900-144297050	GM12878	blood:	n/a	n/a
40	CTCF	chr4:144296901-144297078	LNCaP	prostate:	n/a	n/a
41	CTCF	chr4:144296920-144297070	GM12873	blood:	n/a	n/a
42	EP300	chr4:144296555-144296970	K562	blood:	n/a	n/a
43	CTCF	chr4:144296890-144297128	MCF-7	breast:	n/a	n/a
44	CTCF	chr4:144296920-144297070	GM12801	blood:	n/a	n/a
45	CTCF	chr4:144296873-144297132	T-47D	breast:	n/a	n/a
46	WRNIP1	chr4:144296570-144297166	GM12878	blood:	n/a	n/a
47	CTCF	chr4:144296920-144297070	HPAF	blood vessel:	n/a	n/a
48	CTCF	chr4:144296867-144297128	Fibrobl	skin:	n/a	n/a
49	CTCF	chr4:144296815-144297126	HepG2	liver:	n/a	n/a
50	CTCF	chr4:144296880-144297030	HFF-Myc	foreskin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:144292852..144297100-chr4:144298409..144302941,5	K562	blood:
2	chr4:144257935..144259880-chr4:144296110..144298167,2	MCF-7	breast:
3	chr4:144290996..144292995-chr4:144295055..144297084,2	MCF-7	breast:
4	chr4:144296798..144297742-chr4:144403694..144404468,2	MCF-7	breast:

Variant related genes	Relation type
GAB1	TF binding region
ENSG00000109458	Chromatin interaction
ENSG00000178972	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2323011	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28925882	0.82[AFR][1000 genomes]
rs28925887	0.82[AFR][1000 genomes]
rs28989215	1.00[EUR][1000 genomes]
rs28989224	1.00[EUR][1000 genomes]
rs28989225	1.00[EUR][1000 genomes]
rs28989230	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62337486	0.89[EUR][1000 genomes]
rs62337489	0.89[EUR][1000 genomes]
rs62337511	0.89[EUR][1000 genomes]
rs62337512	0.80[EUR][1000 genomes]
rs62337513	0.89[EUR][1000 genomes]
rs62337514	0.89[EUR][1000 genomes]
rs62337515	1.00[EUR][1000 genomes]
rs62337516	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62337517	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62337518	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62337519	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62337524	1.00[EUR][1000 genomes]
rs62337525	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62337526	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62337527	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62337528	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62337529	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62337530	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62337531	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62337532	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6828635	1.00[EUR][1000 genomes]
rs745164	0.89[EUR][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	nsv1018566	chr4:144284927-144298930	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
2	nsv1021714	chr4:144288438-144299191	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
3	nsv1033347	chr4:144288438-144299563	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144272800-144299800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:144283000-144302200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:144284400-144299400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:144286000-144298200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:144291000-144299800	Weak transcription	Pancreas	Pancrea
6	chr4:144291600-144299400	Weak transcription	Fetal Intestine Large	intestine
7	chr4:144291800-144302200	Weak transcription	Esophagus	oesophagus
8	chr4:144293200-144298000	Enhancers	Fetal Heart	heart
9	chr4:144293200-144299400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:144293200-144299800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr4:144293200-144302400	Enhancers	Brain Substantia Nigra	brain
12	chr4:144293400-144298200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr4:144293600-144302000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:144294000-144302200	Weak transcription	Spleen	Spleen
15	chr4:144294000-144302400	Weak transcription	Gastric	stomach
16	chr4:144294400-144297400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:144294800-144297200	Enhancers	Ovary	ovary
18	chr4:144295000-144302800	Enhancers	Brain Cingulate Gyrus	brain
19	chr4:144295200-144297400	Enhancers	K562	blood
20	chr4:144295200-144298200	Enhancers	Primary B cells from cord blood	blood
21	chr4:144295200-144301000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:144295200-144302400	Enhancers	Brain Anterior Caudate	brain
23	chr4:144295400-144297200	Enhancers	Fetal Brain Female	brain
24	chr4:144295400-144299600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr4:144295400-144300000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr4:144295400-144300200	Enhancers	Fetal Brain Male	brain
27	chr4:144295400-144301000	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr4:144295400-144302000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:144295600-144297000	Weak transcription	Brain Germinal Matrix	brain
30	chr4:144295600-144297000	Enhancers	Duodenum Mucosa	Duodenum
31	chr4:144295600-144297200	Enhancers	Fetal Stomach	stomach
32	chr4:144295600-144297200	Enhancers	Psoas Muscle	Psoas
33	chr4:144295600-144297200	Enhancers	Osteobl	bone
34	chr4:144295600-144300400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr4:144295600-144300800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr4:144295600-144302400	Enhancers	Rectal Smooth Muscle	rectum
37	chr4:144295600-144303000	Enhancers	Brain Angular Gyrus	brain
38	chr4:144295800-144297000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr4:144295800-144297200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:144295800-144297200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:144295800-144297200	Enhancers	NHLF	lung
42	chr4:144295800-144298200	Enhancers	Placenta	Placenta
43	chr4:144296000-144297200	Enhancers	Left Ventricle	heart
44	chr4:144296000-144297200	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr4:144296000-144299000	Weak transcription	Right Ventricle	heart
46	chr4:144296000-144302200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:144296200-144297000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:144296200-144297000	Enhancers	Stomach Mucosa	stomach
49	chr4:144296200-144297200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr4:144296200-144297200	Genic enhancers	Fetal Intestine Small	intestine

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