Variant report

Variant	rs4723883
Chromosome Location	chr7:39649055-39649056
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	EP300	chr7:39648599-39649302	SK-N-SH_RA	brain:	n/a	n/a
2	FOS	chr7:39648822-39649145	MCF10A-Er-Src	breast:	n/a	n/a
3	TEAD4	chr7:39648599-39649486	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr7:39648496-39649803	HUVEC	blood vessel:	n/a	n/a
5	CEBPB	chr7:39648667-39649318	IMR90	lung:	n/a	chr7:39648848-39648859
6	POLR2A	chr7:39648448-39650115	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr7:39649029-39649058	MCF10A-Er-Src	breast:	n/a	n/a
8	MAX	chr7:39648612-39649540	SK-N-SH	brain:	n/a	chr7:39649309-39649319
9	STAT3	chr7:39648874-39649081	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr7:39648697-39649154	Hela-S3	cervix:	n/a	chr7:39648848-39648859
11	CTCF	chr7:39649020-39649170	BE2_C	brain:	n/a	n/a
12	FOSL2	chr7:39648629-39649361	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr7:39648513-39649461	SK-N-SH	brain:	n/a	n/a
14	TAF1	chr7:39649038-39649306	SK-N-SH	brain:	n/a	n/a
15	GATA2	chr7:39648591-39649940	SH-SY5Y	brain:	n/a	n/a
16	EP300	chr7:39648492-39649331	SK-N-SH	brain:	n/a	n/a
17	TCF12	chr7:39647722-39649489	SK-N-SH	brain:	n/a	n/a
18	TCF12	chr7:39648496-39649466	SK-N-SH	brain:	n/a	n/a
19	JUND	chr7:39648481-39649357	SK-N-SH	brain:	n/a	chr7:39648528-39648538
20	PBX3	chr7:39648527-39649511	SK-N-SH	brain:	n/a	n/a
21	FOS	chr7:39648847-39649111	MCF10A-Er-Src	breast:	n/a	n/a
22	MAFF	chr7:39649028-39649136	HepG2	liver:	n/a	n/a
23	FOS	chr7:39647889-39649907	HUVEC	blood vessel:	n/a	chr7:39648528-39648538
24	MAX	chr7:39648548-39649939	SK-N-SH	brain:	n/a	chr7:39649309-39649319
25	POLR2A	chr7:39648836-39649659	IMR90	lung:	n/a	n/a
26	JUND	chr7:39648586-39649387	SK-N-SH	brain:	n/a	n/a
27	GATA3	chr7:39648762-39649220	SH-SY5Y	brain:	n/a	n/a
28	FOS	chr7:39648822-39649139	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr7:39647773-39650312	HUVEC	blood vessel:	n/a	n/a
30	EP300	chr7:39648461-39649526	SK-N-SH	brain:	n/a	n/a
31	PBX3	chr7:39648607-39649409	SK-N-SH	brain:	n/a	n/a
32	EP300	chr7:39648744-39649150	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr7:39648614-39649237	SK-N-SH	brain:	n/a	n/a
34	TEAD4	chr7:39648542-39649655	SK-N-SH	brain:	n/a	n/a
35	FOSL2	chr7:39648646-39649260	SK-N-SH	brain:	n/a	n/a
36	MEF2A	chr7:39648641-39649258	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr7:39647664-39650225	HUVEC	blood vessel:	n/a	n/a
38	SPI1	chr7:39648997-39649463	HL-60	blood:	n/a	n/a
39	GATA3	chr7:39647612-39650090	SK-N-SH	brain:	n/a	chr7:39648117-39648124 chr7:39648352-39648361 chr7:39648349-39648365 chr7:39648222-39648232 chr7:39648115-39648124 chr7:39648117-39648124 chr7:39648350-39648363 chr7:39648117-39648124 chr7:39648116-39648124
40	POLR2A	chr7:39648997-39649094	MCF10A-Er-Src	breast:	n/a	n/a
41	GATA3	chr7:39647622-39649486	SK-N-SH	brain:	n/a	chr7:39648117-39648124 chr7:39648352-39648361 chr7:39648349-39648365 chr7:39648222-39648232 chr7:39648115-39648124 chr7:39648117-39648124 chr7:39648350-39648363 chr7:39648117-39648124 chr7:39648116-39648124
42	JUN	chr7:39648629-39649271	HUVEC	blood vessel:	n/a	n/a
43	GATA2	chr7:39647563-39649910	HUVEC	blood vessel:	n/a	chr7:39648117-39648124 chr7:39648352-39648361 chr7:39648349-39648365 chr7:39648222-39648232 chr7:39648115-39648124 chr7:39648117-39648124 chr7:39648350-39648363 chr7:39648117-39648124
44	MAFK	chr7:39648496-39649242	IMR90	lung:	n/a	chr7:39648527-39648537
45	EP300	chr7:39647430-39650405	SK-N-SH	brain:	n/a	chr7:39648095-39648109 chr7:39648066-39648080 chr7:39648065-39648079
46	POLR2A	chr7:39648588-39649571	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39643975..39649260-chr7:39661579..39666438,6	K562	blood:

Variant related genes	Relation type
ENSG00000106540	TF binding region
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10245247	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10258946	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10266149	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486798	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486800	1.00[CEU][hapmap]
rs12111908	0.98[ASN][1000 genomes]
rs17171603	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs17416652	1.00[CEU][hapmap]
rs17507685	1.00[CEU][hapmap]
rs17507748	1.00[CEU][hapmap]
rs17508696	1.00[CEU][hapmap]
rs17713754	0.82[ASN][1000 genomes]
rs17713951	0.86[ASN][1000 genomes]
rs17714049	0.98[ASN][1000 genomes]
rs17770594	0.82[ASN][1000 genomes]
rs17770612	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs17770625	0.82[ASN][1000 genomes]
rs1989533	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329455	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2329460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2329461	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329462	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4451213	0.84[AMR][1000 genomes]
rs4469364	0.90[AFR][1000 genomes]
rs4720329	0.92[AFR][1000 genomes]
rs4723881	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723882	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723884	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723885	1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58299139	0.82[ASN][1000 genomes]
rs59071947	0.82[ASN][1000 genomes]
rs61493712	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958662	0.93[AFR][1000 genomes]
rs6968742	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73375695	0.82[ASN][1000 genomes]
rs7777173	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7785964	0.82[ASN][1000 genomes]
rs7796063	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7807233	1.00[CEU][hapmap]
rs7809088	0.93[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39643800-39649200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr7:39644800-39649800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:39645200-39649400	Weak transcription	HSMMtube	muscle
4	chr7:39645200-39661600	Weak transcription	A549	lung
5	chr7:39646400-39650000	Enhancers	Stomach Mucosa	stomach
6	chr7:39646800-39649200	Weak transcription	K562	blood
7	chr7:39647000-39649800	Enhancers	Hela-S3	cervix
8	chr7:39647600-39650000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:39647600-39650200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr7:39647800-39649200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:39647800-39649200	Enhancers	NHLF	lung
12	chr7:39647800-39649400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:39647800-39649400	Enhancers	Osteobl	bone
14	chr7:39647800-39649800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:39648000-39649800	Enhancers	Small Intestine	intestine
16	chr7:39648000-39649800	Enhancers	HSMM	muscle
17	chr7:39648000-39650000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr7:39648400-39651800	Flanking Active TSS	HUVEC	blood vessel
19	chr7:39648600-39649200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:39648600-39649200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:39648600-39649200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr7:39648600-39649200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:39648600-39649200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:39648600-39649200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr7:39648600-39649200	Enhancers	Fetal Muscle Leg	muscle
26	chr7:39648600-39649200	Enhancers	Fetal Thymus	thymus
27	chr7:39648600-39649600	Flanking Active TSS	HMEC	breast
28	chr7:39648600-39649800	Enhancers	Spleen	Spleen
29	chr7:39648600-39649800	Flanking Active TSS	NH-A	brain
30	chr7:39648600-39650000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
31	chr7:39648800-39649200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:39648800-39649200	Active TSS	Stomach Smooth Muscle	stomach
33	chr7:39648800-39656000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:39649000-39649200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
35	chr7:39649000-39649200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:39649000-39649200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr7:39649000-39649200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:39649000-39649200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr7:39649000-39649200	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr7:39649000-39649200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:39649000-39649200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr7:39649000-39649200	Enhancers	Esophagus	oesophagus
43	chr7:39649000-39649200	Bivalent Enhancer	Fetal Brain Female	brain
44	chr7:39649000-39649200	Active TSS	Fetal Intestine Large	intestine
45	chr7:39649000-39649200	Active TSS	Left Ventricle	heart
46	chr7:39649000-39649200	Active TSS	Psoas Muscle	Psoas
47	chr7:39649000-39649200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
48	chr7:39649000-39649400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:39649000-39649400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr7:39649000-39649400	Active TSS	Primary T killer memory cells from peripheral blood	blood

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