Variant report

Variant	rs13086868
Chromosome Location	chr3:139239644-139239645
allele	A/G
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	chr3:139238727-139239735	HCT-116	colon:	n/a	chr3:139239093-139239111 chr3:139239421-139239442 chr3:139239095-139239108 chr3:139239088-139239109 chr3:139239419-139239437
2	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
3	CTCF	chr3:139239560-139239710	NHDF-neo	bronchial:	n/a	n/a
4	RAD21	chr3:139238713-139239724	HCT-116	colon:	n/a	chr3:139239091-139239110 chr3:139239095-139239105 chr3:139239094-139239107 chr3:139239420-139239439 chr3:139239093-139239105 chr3:139239059-139239072

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	chr3:139146130..139147006-chr3:139239589..139240160,2	MCF-7	breast:
4	chr3:139233944..139235720-chr3:139238197..139241033,2	K562	blood:

Variant related genes	Relation type
RBP1	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1044826	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10935323	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12494556	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494806	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs12695698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12695699	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12695700	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13060697	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13074208	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13083195	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs13085888	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13089007	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13089052	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089090	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13092507	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13092935	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1586861	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1586863	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1586864	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17336869	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1907687	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2165139	0.98[ASN][1000 genomes]
rs2233811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2233815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2349059	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34623690	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3772877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3821544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3821545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4544576	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683799	0.87[EUR][1000 genomes]
rs4683818	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67929453	0.81[ASN][1000 genomes]
rs747346	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9289578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs964227	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs973691	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9812192	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9818691	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9825064	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9831108	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9834607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9848241	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9849039	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9849578	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9853350	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9860201	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9860521	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9868544	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9882014	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

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:43 , 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	chr3:139236000-139245200	Weak transcription	Brain Anterior Caudate	brain
15	chr3:139236400-139250800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:139236600-139245000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:139236600-139252000	Weak transcription	Right Atrium	heart
18	chr3:139237200-139249600	Weak transcription	Brain Germinal Matrix	brain
19	chr3:139237800-139241400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:139238800-139251600	Weak transcription	Small Intestine	intestine
21	chr3:139239000-139241000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:139239000-139241000	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr3:139239000-139242400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:139239000-139242600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:139239000-139245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:139239000-139247600	Weak transcription	NHEK	skin
27	chr3:139239000-139249600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:139239200-139239800	Strong transcription	Fetal Stomach	stomach
29	chr3:139239200-139244800	Weak transcription	Fetal Lung	lung
30	chr3:139239200-139247400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:139239200-139251400	Weak transcription	Placenta	Placenta
32	chr3:139239400-139239800	Strong transcription	NH-A	brain
33	chr3:139239400-139241200	Weak transcription	Pancreas	Pancrea
34	chr3:139239400-139241600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:139239400-139246400	Weak transcription	Esophagus	oesophagus
36	chr3:139239600-139241200	Weak transcription	Ovary	ovary
37	chr3:139239600-139241400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:139239600-139241400	Weak transcription	Fetal Intestine Small	intestine
39	chr3:139239600-139241400	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:139239600-139244000	Weak transcription	Fetal Intestine Large	intestine
41	chr3:139239600-139250000	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:139239600-139250000	Weak transcription	Brain Substantia Nigra	brain
43	chr3:139239600-139251400	Weak transcription	Duodenum Mucosa	Duodenum

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