Variant report

Variant	rs2594558
Chromosome Location	chr3:81811845-81811846
allele	G/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	POLR2A	chr3:81809125-81813460	GM12878	blood:	n/a	n/a
2	CTCF	chr3:81811760-81811910	HFF-Myc	foreskin:	n/a	n/a
3	MYC	chr3:81809659-81811873	A549	lung:	n/a	chr3:81810948-81810964 chr3:81810392-81810402 chr3:81810858-81810868
4	POLR2A	chr3:81809196-81812982	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:81808535-81812327	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr3:81810039-81811931	K562	blood:	n/a	chr3:81810803-81810819 chr3:81811589-81811603 chr3:81810319-81810335 chr3:81810939-81810955
7	POLR2A	chr3:81809916-81811923	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:81809830-81811942	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:81809258-81811955	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:81809755-81811870	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:81809393-81812042	HUVEC	blood vessel:	n/a	n/a
12	PML	chr3:81809703-81812388	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:81809088-81811920	U87	brain:	n/a	n/a
14	POLR2A	chr3:81808676-81812699	K562	blood:	n/a	n/a
15	POLR2A	chr3:81809950-81811846	K562	blood:	n/a	n/a
16	MTA3	chr3:81809107-81812010	GM12878	blood:	n/a	n/a
17	IRF1	chr3:81811419-81812030	K562	blood:	n/a	chr3:81811590-81811599
18	POLR2A	chr3:81809042-81811944	U87	brain:	n/a	n/a
19	BCLAF1	chr3:81809434-81811914	GM12878	blood:	n/a	chr3:81810803-81810812 chr3:81810798-81810811
20	POLR2A	chr3:81809619-81812556	GM12892	blood:	n/a	n/a
21	POLR2A	chr3:81809042-81811950	U87	brain:	n/a	n/a
22	POLR2A	chr3:81809977-81811899	GM12891	blood:	n/a	n/a
23	GATA1	chr3:81809835-81812043	PBDE	blood:	n/a	chr3:81810197-81810206 chr3:81811002-81811012 chr3:81811569-81811585 chr3:81810787-81810795

No.	Distal block	Cell Line	Cell type
1	chr3:81789146..81795604-chr3:81809193..81811958,7	MCF-7	breast:
2	chr12:121733110..121736069-chr3:81809721..81812341,2	MCF-7	breast:
3	chr3:81789819..81797196-chr3:81807650..81813820,9	K562	blood:

Variant related genes	Relation type
GBE1	TF binding region
ENSG00000110931	Chromatin interaction
ENSG00000114480	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1155277	0.84[AMR][1000 genomes]
rs12495343	0.83[EUR][1000 genomes]
rs12635671	0.82[EUR][1000 genomes]
rs1404297	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1829967	0.87[EUR][1000 genomes]
rs1973800	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1973801	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1997002	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2244294	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2252530	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2594547	0.82[AMR][1000 genomes]
rs2594549	0.84[AMR][1000 genomes]
rs2594551	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2594553	0.84[AMR][1000 genomes]
rs2594562	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680245	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680246	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680257	0.82[AMR][1000 genomes]
rs2680260	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2680264	0.81[AMR][1000 genomes]
rs2680274	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2680277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680280	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691077	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691078	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691079	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691080	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691083	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691084	0.85[EUR][1000 genomes]
rs2691085	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2691089	0.89[EUR][1000 genomes]
rs2691093	0.84[EUR][1000 genomes]
rs3107240	0.82[AMR][1000 genomes]
rs3772889	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6803932	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7611902	0.89[EUR][1000 genomes]
rs950904	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9822266	0.89[EUR][1000 genomes]
rs9832088	0.86[EUR][1000 genomes]
rs9860204	0.89[EUR][1000 genomes]
rs9863009	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1009607	chr3:81651419-81825151	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv536604	chr3:81651419-81825151	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv834749	chr3:81655377-81818880	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv999992	chr3:81693662-82015969	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv536605	chr3:81693662-82015969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81811200-81812400	Enhancers	Brain Germinal Matrix	brain
2	chr3:81811200-81818200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:81811400-81812000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:81811400-81812200	Weak transcription	Left Ventricle	heart
5	chr3:81811400-81812200	Enhancers	HSMM	muscle
6	chr3:81811400-81812400	Enhancers	Liver	Liver
7	chr3:81811400-81813800	Weak transcription	Right Atrium	heart
8	chr3:81811400-81818200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:81811600-81812400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:81811600-81812400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:81811600-81812400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:81811600-81812400	Enhancers	Hela-S3	cervix
13	chr3:81811600-81812600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:81811600-81812600	Enhancers	Fetal Heart	heart
15	chr3:81811600-81812800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:81811600-81813200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr3:81811600-81813200	Enhancers	HepG2	liver
18	chr3:81811600-81814000	Enhancers	Psoas Muscle	Psoas
19	chr3:81811600-81814200	Weak transcription	HSMMtube	muscle
20	chr3:81811800-81812000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:81811800-81812200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:81811800-81812200	Weak transcription	Aorta	Aorta
23	chr3:81811800-81812400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:81811800-81812400	Enhancers	Right Ventricle	heart
25	chr3:81811800-81812600	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr3:81811800-81812600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:81811800-81812600	Enhancers	Dnd41	blood
28	chr3:81811800-81812600	Enhancers	K562	blood
29	chr3:81811800-81812800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:81811800-81813000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:81811800-81813600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:81811800-81813600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:81811800-81814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:81811800-81814800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:81811800-81818200	Weak transcription	Osteobl	bone
36	chr3:81811800-81818600	Weak transcription	NHEK	skin

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