Variant report

Variant	rs295490
Chromosome Location	chr3:139241371-139241372
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	RAD21	chr3:139241202-139241761	HCT-116	colon:	n/a	chr3:139241308-139241317 chr3:139241304-139241323
2	CTCF	chr3:139241360-139241510	HMF	breast:	n/a	n/a
3	CTCF	chr3:139241360-139241510	K562	blood:	n/a	n/a
4	CTCF	chr3:139241360-139241510	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr3:139241340-139241490	WERI-Rb-1	eye:	n/a	n/a
6	CTCF	chr3:139241360-139241510	HepG2	liver:	n/a	n/a
7	CTCF	chr3:139241360-139241510	HVMF	connective:	n/a	n/a
8	CTCF	chr3:139241323-139241530	K562	blood:	n/a	n/a
9	CTCF	chr3:139241340-139241490	HEK293	kidney:	n/a	n/a
10	ZNF143	chr3:139241342-139241597	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:139241360-139241510	HPF	lung:	n/a	n/a
12	CTCF	chr3:139241270-139241601	H1-hESC	embryonic stem cell:	n/a	n/a
13	TEAD4	chr3:139241284-139241562	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr3:139241320-139241470	GM12875	blood:	n/a	n/a
15	CTCF	chr3:139241360-139241510	GM12871	blood:	n/a	n/a
16	CTCF	chr3:139241340-139241490	GM06990	blood:	n/a	n/a
17	RAD21	chr3:139241307-139241642	H1-hESC	embryonic stem cell:	n/a	chr3:139241308-139241317
18	RAD21	chr3:139241261-139241686	HCT-116	colon:	n/a	chr3:139241308-139241317 chr3:139241304-139241323
19	CTCF	chr3:139241320-139241470	GM12872	blood:	n/a	n/a
20	CTCF	chr3:139241320-139241470	Caco-2	colon:	n/a	n/a
21	CTCF	chr3:139241360-139241510	HMEC	breast:	n/a	n/a
22	RAD21	chr3:139241267-139241603	SK-N-SH_RA	brain:	n/a	chr3:139241308-139241317 chr3:139241304-139241323
23	RAD21	chr3:139241331-139241612	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr3:139241320-139241470	BE2_C	brain:	n/a	n/a
25	CTCF	chr3:139241297-139241650	K562	blood:	n/a	n/a
26	RAD21	chr3:139241254-139241656	ECC-1	luminal epithelium:	n/a	chr3:139241308-139241317 chr3:139241304-139241323
27	CTCF	chr3:139241258-139241650	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr3:139241320-139241470	HRE	kidney:	n/a	n/a
29	CTCF	chr3:139241320-139241470	AG04449	skin:	n/a	n/a
30	CTCF	chr3:139241360-139241510	HPAF	blood vessel:	n/a	n/a
31	CTCF	chr3:139241320-139241470	GM12874	blood:	n/a	n/a
32	CTCF	chr3:139241360-139241510	GM12878	blood:	n/a	n/a
33	RAD21	chr3:139241189-139241658	H1-hESC	embryonic stem cell:	n/a	chr3:139241308-139241317 chr3:139241304-139241323
34	CTCF	chr3:139241360-139241510	AG09319	gingival:	n/a	n/a
35	CTCF	chr3:139241360-139241510	NHEK	skin:	n/a	n/a
36	CTCF	chr3:139241340-139241490	HCM	heart:	n/a	n/a
37	CTCF	chr3:139241320-139241470	AoAF	blood vessel:	n/a	n/a
38	CTCF	chr3:139241322-139241561	K562	blood:	n/a	n/a
39	RAD21	chr3:139241369-139241650	ECC-1	luminal epithelium:	n/a	n/a
40	EP300	chr3:139240383-139241735	SK-N-SH	brain:	n/a	n/a
41	YY1	chr3:139241262-139241605	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr3:139241360-139241510	GM12873	blood:	n/a	n/a
43	RAD21	chr3:139241316-139241636	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139239944..139241919-chr3:139253042..139255747,2	MCF-7	breast:

Variant related genes	Relation type
RBP1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10513063	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs1602626	0.81[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs1602628	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs1610195	0.91[CHD][hapmap]
rs17335312	0.89[CEU][hapmap]
rs17395611	0.81[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs17494356	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs17560106	0.89[CEU][hapmap]
rs184156	1.00[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs184157	1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2289350	0.81[CEU][hapmap]
rs2291555	0.86[CEU][hapmap]
rs2307031	0.81[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs295489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772871	0.81[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs3772876	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs397940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41356949	0.81[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs41399544	0.81[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs9289573	0.91[CHD][hapmap]
rs9821204	0.82[JPT][hapmap]
rs9848910	0.91[CHD][hapmap]
rs9862672	0.82[JPT][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

Variant related diseases (count:1)

Disease	PMID	Source
PR interval in Tripanosoma cruzi seropositivity	24324551	GWAS catalog

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	chr3:139234400-139252600	Weak transcription	Lung	lung
8	chr3:139234800-139250600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:139234800-139251000	Weak transcription	Fetal Kidney	kidney
10	chr3:139234800-139251200	Weak transcription	Fetal Heart	heart
11	chr3:139235000-139253600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:139235200-139251400	Weak transcription	Liver	Liver
13	chr3:139236000-139245200	Weak transcription	Brain Anterior Caudate	brain
14	chr3:139236400-139250800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:139236600-139245000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:139236600-139252000	Weak transcription	Right Atrium	heart
17	chr3:139237200-139249600	Weak transcription	Brain Germinal Matrix	brain
18	chr3:139237800-139241400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:139238800-139251600	Weak transcription	Small Intestine	intestine
20	chr3:139239000-139242400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:139239000-139242600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:139239000-139245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:139239000-139247600	Weak transcription	NHEK	skin
24	chr3:139239000-139249600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:139239200-139244800	Weak transcription	Fetal Lung	lung
26	chr3:139239200-139247400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:139239200-139251400	Weak transcription	Placenta	Placenta
28	chr3:139239400-139241600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:139239400-139246400	Weak transcription	Esophagus	oesophagus
30	chr3:139239600-139241400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:139239600-139241400	Weak transcription	Fetal Intestine Small	intestine
32	chr3:139239600-139241400	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:139239600-139244000	Weak transcription	Fetal Intestine Large	intestine
34	chr3:139239600-139250000	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:139239600-139250000	Weak transcription	Brain Substantia Nigra	brain
36	chr3:139239600-139251400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:139240600-139248600	Strong transcription	NH-A	brain
38	chr3:139240600-139251000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:139240800-139241400	Genic enhancers	Fetal Stomach	stomach
40	chr3:139240800-139251800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:139241200-139241400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr3:139241200-139241400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr3:139241200-139241400	Enhancers	Fetal Brain Male	brain
44	chr3:139241200-139241800	Enhancers	Pancreas	Pancrea
45	chr3:139241200-139242400	Strong transcription	Ovary	ovary
46	chr3:139241200-139245400	Weak transcription	Fetal Brain Female	brain

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