Variant report

Variant	rs2594553
Chromosome Location	chr3:81793085-81793086
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	BCL3	chr3:81792192-81793340	A549	lung:	n/a	chr3:81792698-81792707
2	FOS	chr3:81791877-81793096	MCF10A-Er-Src	breast:	n/a	chr3:81792298-81792308 chr3:81792534-81792546 chr3:81792297-81792308 chr3:81792297-81792309 chr3:81792299-81792307 chr3:81792427-81792439 chr3:81792298-81792308
3	CEBPB	chr3:81792188-81793284	A549	lung:	n/a	n/a
4	JUN	chr3:81791732-81794075	K562	blood:	n/a	chr3:81792298-81792308 chr3:81792534-81792546 chr3:81793639-81793648 chr3:81792297-81792309 chr3:81792299-81792307 chr3:81792427-81792439 chr3:81792298-81792308
5	SP1	chr3:81792025-81793288	A549	lung:	n/a	n/a
6	RCOR1	chr3:81791675-81794122	IMR90	lung:	n/a	n/a
7	TCF12	chr3:81792467-81793192	A549	lung:	n/a	n/a
8	CHD1	chr3:81791710-81794472	IMR90	lung:	n/a	n/a
9	NFATC1	chr3:81792576-81793208	GM12878	blood:	n/a	n/a
10	GATA3	chr3:81791963-81794163	A549	lung:	n/a	chr3:81793773-81793782 chr3:81793663-81793672 chr3:81793769-81793785 chr3:81793770-81793780 chr3:81793773-81793782 chr3:81793772-81793782 chr3:81793687-81793696 chr3:81793134-81793142
11	MAX	chr3:81792141-81793230	A549	lung:	n/a	chr3:81792698-81792707
12	USF1	chr3:81792454-81793202	A549	lung:	n/a	n/a
13	JUND	chr3:81791680-81793344	SK-N-SH	brain:	n/a	chr3:81792298-81792308 chr3:81792534-81792546 chr3:81792297-81792309 chr3:81792299-81792307 chr3:81792427-81792439 chr3:81792697-81792708 chr3:81792298-81792308
14	FOS	chr3:81791952-81793089	HUVEC	blood vessel:	n/a	chr3:81792298-81792308 chr3:81792534-81792546 chr3:81792297-81792308 chr3:81792297-81792309 chr3:81792299-81792307 chr3:81792427-81792439 chr3:81792298-81792308
15	RCOR1	chr3:81792235-81793108	K562	blood:	n/a	n/a
16	POLR2A	chr3:81791713-81793291	U87	brain:	n/a	n/a
17	BCL3	chr3:81792138-81793126	A549	lung:	n/a	chr3:81792698-81792707
18	JUN	chr3:81792117-81793110	HUVEC	blood vessel:	n/a	chr3:81792298-81792308 chr3:81792534-81792546 chr3:81792297-81792309 chr3:81792299-81792307 chr3:81792427-81792439 chr3:81792298-81792308
19	GATA2	chr3:81792232-81793140	HUVEC	blood vessel:	n/a	n/a
20	EP300	chr3:81792256-81793294	K562	blood:	n/a	chr3:81792520-81792534 chr3:81792698-81792707
21	JUND	chr3:81791991-81793138	SK-N-SH	brain:	n/a	chr3:81792298-81792308 chr3:81792534-81792546 chr3:81792297-81792309 chr3:81792299-81792307 chr3:81792427-81792439 chr3:81792697-81792708 chr3:81792298-81792308
22	POLR2A	chr3:81791798-81793092	U87	brain:	n/a	n/a
23	JUND	chr3:81792498-81793279	A549	lung:	n/a	chr3:81792534-81792546 chr3:81792697-81792708
24	GATA3	chr3:81792490-81793343	A549	lung:	n/a	chr3:81793134-81793142
25	FOXA2	chr3:81792803-81793220	A549	lung:	n/a	n/a
26	GATA3	chr3:81792115-81793105	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr3:81792679-81793097	GM12878	blood:	n/a	n/a
28	BHLHE40	chr3:81792494-81793380	K562	blood:	n/a	n/a
29	MAX	chr3:81792044-81793272	A549	lung:	n/a	chr3:81792698-81792707
30	FOSL2	chr3:81791996-81793091	SK-N-SH	brain:	n/a	chr3:81792298-81792308 chr3:81792534-81792546 chr3:81792297-81792309 chr3:81792299-81792307 chr3:81792427-81792439 chr3:81792298-81792308
31	NFIC	chr3:81792183-81793094	SK-N-SH	brain:	n/a	n/a
32	TCF12	chr3:81792003-81793189	SK-N-SH	brain:	n/a	n/a
33	REST	chr3:81792067-81793231	A549	lung:	n/a	n/a
34	SP1	chr3:81791994-81794290	A549	lung:	n/a	n/a
35	STAT3	chr3:81792288-81793101	Hela-S3	cervix:	n/a	n/a
36	TCF12	chr3:81791929-81794188	A549	lung:	n/a	n/a
37	EP300	chr3:81791964-81794065	A549	lung:	n/a	chr3:81792520-81792534 chr3:81792698-81792707
38	GATA3	chr3:81791959-81793306	SK-N-SH	brain:	n/a	chr3:81793134-81793142
39	FOSL2	chr3:81791896-81794099	A549	lung:	n/a	chr3:81792298-81792308 chr3:81792534-81792546 chr3:81793639-81793648 chr3:81792297-81792309 chr3:81792299-81792307 chr3:81792427-81792439 chr3:81792298-81792308
40	FOSL2	chr3:81792167-81793106	A549	lung:	n/a	chr3:81792298-81792308 chr3:81792534-81792546 chr3:81792297-81792309 chr3:81792299-81792307 chr3:81792427-81792439 chr3:81792298-81792308
41	TCF12	chr3:81792016-81793246	SK-N-SH	brain:	n/a	n/a
42	GATA1	chr3:81792232-81793900	PBDE	blood:	n/a	chr3:81793773-81793782 chr3:81793663-81793672 chr3:81793769-81793785 chr3:81793770-81793780 chr3:81793773-81793782 chr3:81793772-81793782 chr3:81793687-81793696 chr3:81793134-81793142
43	EP300	chr3:81792033-81793360	A549	lung:	n/a	chr3:81792520-81792534 chr3:81792698-81792707
44	EP300	chr3:81792083-81793147	SK-N-SH	brain:	n/a	chr3:81792520-81792534 chr3:81792698-81792707
45	RCOR1	chr3:81792339-81793276	K562	blood:	n/a	n/a
46	NFIC	chr3:81792016-81793211	SK-N-SH	brain:	n/a	n/a
47	FOS	chr3:81792112-81793138	MCF10A-Er-Src	breast:	n/a	chr3:81792298-81792308 chr3:81792534-81792546 chr3:81792297-81792308 chr3:81792297-81792309 chr3:81792299-81792307 chr3:81792427-81792439 chr3:81792298-81792308
48	FOXA2	chr3:81792568-81793375	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:81792798..81795144-chr3:81808070..81811820,3	MCF-7	breast:
2	chr3:81789146..81795604-chr3:81809193..81811958,7	MCF-7	breast:
3	chr3:81789819..81797196-chr3:81807650..81813820,9	K562	blood:

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

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11127737	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1155277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1375086	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2594547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2594549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2594551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2594558	0.84[AMR][1000 genomes]
rs2594562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs2680245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2680246	0.84[AMR][1000 genomes]
rs2680257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2680260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2680264	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2680277	0.96[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2680280	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs2691093	0.96[CEU][hapmap]
rs3107240	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772899	0.96[CEU][hapmap]
rs3772902	0.96[CEU][hapmap]
rs6771266	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6803932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7648237	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9309876	0.81[AMR][1000 genomes]
rs9818090	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9852545	0.86[AMR][1000 genomes]
rs9860805	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81776000-81807400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:81781000-81809400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:81782200-81800400	Weak transcription	Primary B cells from cord blood	blood
4	chr3:81782400-81800200	Weak transcription	Left Ventricle	heart
5	chr3:81782800-81796600	Weak transcription	Right Atrium	heart
6	chr3:81789200-81794400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:81789600-81793600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:81789600-81794400	Enhancers	Fetal Heart	heart
9	chr3:81789600-81794600	Enhancers	Hela-S3	cervix
10	chr3:81789600-81794800	Enhancers	Adipose Nuclei	Adipose
11	chr3:81790000-81793400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:81790600-81793200	Enhancers	Colon Smooth Muscle	Colon
13	chr3:81791000-81793400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:81791200-81793800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:81791200-81794800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:81791200-81794800	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr3:81791200-81794800	Enhancers	Liver	Liver
18	chr3:81791200-81808800	Weak transcription	Primary T cells from cord blood	blood
19	chr3:81791400-81795400	Weak transcription	Right Ventricle	heart
20	chr3:81791400-81796400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:81791600-81793200	Enhancers	Rectal Smooth Muscle	rectum
22	chr3:81791600-81793400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:81791600-81794400	Enhancers	K562	blood
24	chr3:81791600-81803400	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:81791800-81793400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:81791800-81794000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr3:81791800-81794000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr3:81791800-81794600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:81792000-81794000	Enhancers	Stomach Mucosa	stomach
30	chr3:81792000-81795000	Enhancers	HSMM	muscle
31	chr3:81792000-81795400	Weak transcription	Psoas Muscle	Psoas
32	chr3:81792000-81810200	Weak transcription	Spleen	Spleen
33	chr3:81792200-81793800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr3:81792200-81793800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:81792200-81794000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:81792200-81794200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:81792200-81794400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:81792200-81794800	Enhancers	HMEC	breast
39	chr3:81792200-81795200	Enhancers	Osteobl	bone
40	chr3:81792200-81795600	Enhancers	NHLF	lung
41	chr3:81792400-81793600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:81792400-81793800	Enhancers	Stomach Smooth Muscle	stomach
43	chr3:81792400-81795400	Weak transcription	Ovary	ovary
44	chr3:81792600-81793200	Enhancers	Placenta	Placenta
45	chr3:81792600-81793600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:81792600-81793800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:81792600-81793800	Genic enhancers	Dnd41	blood
48	chr3:81792600-81794000	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr3:81792600-81794400	Flanking Active TSS	A549	lung
50	chr3:81792800-81793200	Enhancers	HUES6 Cell Line	embryonic stem cell

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