Variant report

Variant	rs295488
Chromosome Location	chr3:139239323-139239324
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	chr3:139239320-139239470	HMF	breast:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
2	MYC	chr3:139238927-139239512	Hela-S3	cervix:	n/a	chr3:139239158-139239168
3	CTCF	chr3:139239280-139239430	HFF	foreskin:	n/a	n/a
4	CTCF	chr3:139239300-139239450	AG10803	skin:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
5	CTCF	chr3:139239316-139239522	MCF-7	breast:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
6	CTCF	chr3:139238727-139239735	HCT-116	colon:	n/a	chr3:139239093-139239111 chr3:139239421-139239442 chr3:139239095-139239108 chr3:139239088-139239109 chr3:139239419-139239437
7	CTCF	chr3:139239300-139239450	HVMF	connective:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
8	CTCF	chr3:139239035-139239585	IMR90	lung:	n/a	chr3:139239093-139239111 chr3:139239421-139239442 chr3:139239095-139239108 chr3:139239088-139239109 chr3:139239419-139239437
9	MYC	chr3:139238909-139239323	K562	blood:	n/a	chr3:139239158-139239168
10	MAX	chr3:139238907-139239378	H1-hESC	embryonic stem cell:	n/a	chr3:139239158-139239168
11	CTCF	chr3:139239320-139239470	Caco-2	colon:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
12	CTCF	chr3:139238987-139239588	MCF-7	breast:	n/a	chr3:139239093-139239111 chr3:139239421-139239442 chr3:139239095-139239108 chr3:139239088-139239109 chr3:139239419-139239437
13	MYC	chr3:139238921-139239330	K562	blood:	n/a	chr3:139239158-139239168
14	MAX	chr3:139238816-139239401	ECC-1	luminal epithelium:	n/a	chr3:139239158-139239168
15	ATF1	chr3:139238917-139239478	K562	blood:	n/a	n/a
16	MAX	chr3:139238940-139239369	H1-hESC	embryonic stem cell:	n/a	chr3:139239158-139239168
17	CTCF	chr3:139239300-139239450	HAc	cerebellar:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
18	RAD21	chr3:139238766-139239632	SK-N-SH	brain:	n/a	chr3:139239091-139239110 chr3:139239095-139239105 chr3:139239094-139239107 chr3:139239420-139239439 chr3:139239093-139239105 chr3:139239059-139239072
19	MAX	chr3:139238943-139239458	NB4	blood:	n/a	chr3:139239158-139239168
20	RAD21	chr3:139238757-139239724	HCT-116	colon:	n/a	chr3:139239091-139239110 chr3:139239095-139239105 chr3:139239094-139239107 chr3:139239420-139239439 chr3:139239093-139239105 chr3:139239059-139239072
21	RAD21	chr3:139238930-139239493	HepG2	liver:	n/a	chr3:139239091-139239110 chr3:139239095-139239105 chr3:139239094-139239107 chr3:139239420-139239439 chr3:139239093-139239105 chr3:139239059-139239072
22	MAX	chr3:139238890-139239364	MCF-7	breast:	n/a	chr3:139239158-139239168
23	USF1	chr3:139238770-139239353	K562	blood:	n/a	n/a
24	CBX3	chr3:139238791-139239366	K562	blood:	n/a	n/a
25	RAD21	chr3:139239255-139239616	SK-N-SH_RA	brain:	n/a	chr3:139239420-139239439
26	MYC	chr3:139238870-139239516	K562	blood:	n/a	chr3:139239158-139239168
27	RAD21	chr3:139238924-139239618	H1-hESC	embryonic stem cell:	n/a	chr3:139239091-139239110 chr3:139239095-139239105 chr3:139239094-139239107 chr3:139239420-139239439 chr3:139239093-139239105 chr3:139239059-139239072
28	MAX	chr3:139238719-139239355	ECC-1	luminal epithelium:	n/a	chr3:139239158-139239168
29	CTCF	chr3:139238820-139239425	K562	blood:	n/a	chr3:139239093-139239111 chr3:139239095-139239108 chr3:139239088-139239109
30	CTCF	chr3:139239300-139239450	SK-N-SH_RA	brain:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
31	TBP	chr3:139238887-139239368	K562	blood:	n/a	n/a
32	CTCF	chr3:139239320-139239470	GM12873	blood:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
33	MAX	chr3:139238729-139239507	K562	blood:	n/a	chr3:139239158-139239168
34	CTCF	chr3:139239320-139239470	HMEC	breast:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
35	RAD21	chr3:139238874-139239581	ECC-1	luminal epithelium:	n/a	chr3:139239091-139239110 chr3:139239095-139239105 chr3:139239094-139239107 chr3:139239420-139239439 chr3:139239093-139239105 chr3:139239059-139239072
36	CTCF	chr3:139238822-139239586	HCT-116	colon:	n/a	chr3:139239093-139239111 chr3:139239421-139239442 chr3:139239095-139239108 chr3:139239088-139239109 chr3:139239419-139239437
37	RAD21	chr3:139239103-139239631	Hela-S3	cervix:	n/a	chr3:139239420-139239439
38	CTCF	chr3:139239320-139239470	HBMEC	blood vessel:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
39	CTCF	chr3:139239300-139239450	AG04450	lung:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
40	MAX	chr3:139238928-139239575	Hela-S3	cervix:	n/a	chr3:139239158-139239168
41	RAD21	chr3:139239302-139239554	H1-hESC	embryonic stem cell:	n/a	chr3:139239420-139239439
42	CTCF	chr3:139239320-139239470	AG09319	gingival:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
43	CTCF	chr3:139239300-139239450	GM12865	blood:	n/a	chr3:139239421-139239442 chr3:139239419-139239437
44	RAD21	chr3:139238836-139239580	MCF-7	breast:	n/a	chr3:139239091-139239110 chr3:139239095-139239105 chr3:139239094-139239107 chr3:139239420-139239439 chr3:139239093-139239105 chr3:139239059-139239072
45	CTCF	chr3:139239260-139239410	HCM	heart:	n/a	n/a
46	POLR2A	chr3:139238628-139239357	HCT-116	colon:	n/a	n/a
47	RAD21	chr3:139238723-139239612	ECC-1	luminal epithelium:	n/a	chr3:139239091-139239110 chr3:139239095-139239105 chr3:139239094-139239107 chr3:139239420-139239439 chr3:139239093-139239105 chr3:139239059-139239072
48	RAD21	chr3:139239020-139239599	IMR90	lung:	n/a	chr3:139239091-139239110 chr3:139239095-139239105 chr3:139239094-139239107 chr3:139239420-139239439 chr3:139239093-139239105 chr3:139239059-139239072
49	RAD21	chr3:139238887-139239632	H1-hESC	embryonic stem cell:	n/a	chr3:139239091-139239110 chr3:139239095-139239105 chr3:139239094-139239107 chr3:139239420-139239439 chr3:139239093-139239105 chr3:139239059-139239072
50	RAD21	chr3:139239285-139239490	GM12878	blood:	n/a	chr3:139239420-139239439

No.	Distal block	Cell Line	Cell type
1	chr3:139220213..139222626-chr3:139237544..139240385,2	MCF-7	breast:
2	chr3:139239011..139239667-chr3:139271421..139272112,2	MCF-7	breast:
3	chr3:139146193..139146816-chr3:139238621..139239555,2	MCF-7	breast:
4	chr3:139149320..139150091-chr3:139238870..139239588,2	MCF-7	breast:
5	chr3:139233944..139235720-chr3:139238197..139241033,2	K562	blood:

Variant related genes	Relation type
RBP1	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10935322	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs10935328	0.92[AFR][1000 genomes]
rs11705700	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs11706576	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs11920890	1.00[YRI][hapmap]
rs12495890	0.92[AFR][1000 genomes]
rs13064670	0.84[AFR][1000 genomes]
rs13313904	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs13326837	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs13327001	1.00[YRI][hapmap]
rs13327467	0.87[CEU][hapmap]
rs13434189	0.90[ASW][hapmap];0.81[CEU][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs1371338	0.97[AFR][1000 genomes]
rs1371339	0.89[AFR][1000 genomes]
rs1583743	0.90[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1586862	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs17395255	0.90[ASW][hapmap];0.81[CEU][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs17395304	0.90[ASW][hapmap];0.81[CEU][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs176984	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs188422	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs192687	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs211582	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs211585	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2118980	0.97[AFR][1000 genomes]
rs2289347	0.97[AFR][1000 genomes]
rs2289349	0.97[AFR][1000 genomes]
rs2349058	0.83[AFR][1000 genomes]
rs295472	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs295480	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs295483	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs295486	0.89[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34680708	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3555	0.97[AFR][1000 genomes]
rs35674260	0.90[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs387987	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4302343	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4428138	0.97[AFR][1000 genomes]
rs444264	0.90[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4563370	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4683608	0.86[AFR][1000 genomes]
rs6439861	0.97[AFR][1000 genomes]
rs6439862	0.90[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs6778992	0.92[AFR][1000 genomes]
rs6782957	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6804877	0.82[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7372124	0.90[ASW][hapmap];0.81[CEU][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs7372811	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs7373116	0.90[ASW][hapmap];0.81[CEU][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs7374317	0.90[ASW][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs7374348	0.81[CEU][hapmap]
rs7626658	0.83[AFR][1000 genomes]
rs7833	0.90[ASW][hapmap];0.81[CEU][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs9289579	0.97[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs978835	0.90[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs9819368	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs9821875	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs9821891	0.90[ASW][hapmap];0.81[CEU][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs9828954	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs9831144	0.82[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9850987	0.90[ASW][hapmap];0.81[CEU][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs9851318	0.90[ASW][hapmap];0.81[CEU][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs9857390	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs9871030	0.90[ASW][hapmap];0.81[CEU][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs9876640	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1001460	chr3:139194633-139241616	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139208200-139249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:139223000-139247000	Weak transcription	Left Ventricle	heart
3	chr3:139228600-139245000	Weak transcription	Spleen	Spleen
4	chr3:139228800-139253200	Weak transcription	Gastric	stomach
5	chr3:139231000-139252800	Weak transcription	Right Ventricle	heart
6	chr3:139232400-139244400	Weak transcription	HSMMtube	muscle
7	chr3:139233800-139241200	Weak transcription	Fetal Brain Male	brain
8	chr3:139234400-139252600	Weak transcription	Lung	lung
9	chr3:139234800-139250600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:139234800-139251000	Weak transcription	Fetal Kidney	kidney
11	chr3:139234800-139251200	Weak transcription	Fetal Heart	heart
12	chr3:139235000-139253600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:139235200-139251400	Weak transcription	Liver	Liver
14	chr3:139236000-139239400	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr3:139236000-139245200	Weak transcription	Brain Anterior Caudate	brain
16	chr3:139236400-139250800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:139236600-139245000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:139236600-139252000	Weak transcription	Right Atrium	heart
19	chr3:139236800-139239400	Weak transcription	NH-A	brain
20	chr3:139237200-139249600	Weak transcription	Brain Germinal Matrix	brain
21	chr3:139237600-139239600	Genic enhancers	Fetal Intestine Small	intestine
22	chr3:139237800-139241400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:139238200-139239600	Enhancers	Fetal Intestine Large	intestine
24	chr3:139238400-139239600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr3:139238400-139239600	Genic enhancers	Ovary	ovary
26	chr3:139238600-139239400	Genic enhancers	Pancreas	Pancrea
27	chr3:139238600-139239600	Enhancers	Duodenum Mucosa	Duodenum
28	chr3:139238800-139239400	Enhancers	Esophagus	oesophagus
29	chr3:139238800-139251600	Weak transcription	Small Intestine	intestine
30	chr3:139239000-139239600	Enhancers	Brain Cingulate Gyrus	brain
31	chr3:139239000-139239600	Enhancers	Brain Hippocampus Middle	brain
32	chr3:139239000-139239600	Enhancers	Brain Substantia Nigra	brain
33	chr3:139239000-139239600	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:139239000-139239600	Enhancers	K562	blood
35	chr3:139239000-139241000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:139239000-139241000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:139239000-139242400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:139239000-139242600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:139239000-139245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:139239000-139247600	Weak transcription	NHEK	skin
41	chr3:139239000-139249600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:139239200-139239400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr3:139239200-139239800	Strong transcription	Fetal Stomach	stomach
44	chr3:139239200-139244800	Weak transcription	Fetal Lung	lung
45	chr3:139239200-139247400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:139239200-139251400	Weak transcription	Placenta	Placenta

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