Variant report

Variant	rs704580
Chromosome Location	chr3:98484688-98484689
allele	C/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	chr3:98484393-98484996	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr3:98484397-98484968	SK-N-SH_RA	brain:	n/a	n/a
3	TCF12	chr3:98484332-98485059	SK-N-SH	brain:	n/a	n/a
4	YY1	chr3:98484570-98484965	SK-N-SH_RA	brain:	n/a	chr3:98484797-98484806
5	GATA3	chr3:98484530-98484949	SK-N-SH	brain:	n/a	chr3:98484667-98484676
6	GATA3	chr3:98484559-98484815	SH-SY5Y	brain:	n/a	chr3:98484667-98484676
7	YY1	chr3:98484597-98484984	SK-N-SH_RA	brain:	n/a	chr3:98484797-98484806
8	GATA3	chr3:98484322-98485079	SK-N-SH	brain:	n/a	chr3:98484667-98484676
9	RAD21	chr3:98484656-98484905	SK-N-SH_RA	brain:	n/a	n/a
10	EP300	chr3:98480342-98485306	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr3:98484429-98485014	SK-N-SH	brain:	n/a	n/a
12	GATA2	chr3:98484481-98485044	HUVEC	blood vessel:	n/a	chr3:98484667-98484676
13	GATA2	chr3:98484551-98484964	SH-SY5Y	brain:	n/a	chr3:98484667-98484676
14	FOS	chr3:98484645-98485044	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1666291	0.89[EUR][1000 genomes]
rs1666310	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278372	0.93[EUR][1000 genomes]
rs828585	0.81[EUR][1000 genomes]
rs828587	0.81[EUR][1000 genomes]
rs828591	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs828600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98475400-98489400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:98476400-98489400	Weak transcription	HepG2	liver
3	chr3:98477000-98490200	Enhancers	Fetal Heart	heart
4	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:98479000-98485800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:98480800-98489400	Weak transcription	Stomach Mucosa	stomach
7	chr3:98481000-98486200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:98481600-98484800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr3:98481800-98485000	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:98482200-98487800	Weak transcription	Fetal Kidney	kidney
11	chr3:98482200-98495800	Weak transcription	Dnd41	blood
12	chr3:98482400-98485600	Weak transcription	Brain Angular Gyrus	brain
13	chr3:98482400-98489000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:98482400-98496000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:98482600-98485200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr3:98482600-98494600	Weak transcription	Aorta	Aorta
17	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
18	chr3:98482800-98484800	Enhancers	HUVEC	blood vessel
19	chr3:98482800-98497400	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:98483000-98485800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:98483000-98486000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:98483000-98497400	Weak transcription	Spleen	Spleen
23	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:98483200-98485600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:98483600-98484800	Enhancers	Adipose Nuclei	Adipose
27	chr3:98483600-98485400	Weak transcription	Right Ventricle	heart
28	chr3:98483600-98489000	Weak transcription	Thymus	Thymus
29	chr3:98483600-98489200	Weak transcription	Lung	lung
30	chr3:98483600-98489200	Weak transcription	Pancreas	Pancrea
31	chr3:98483600-98489200	Weak transcription	Right Atrium	heart
32	chr3:98483600-98495200	Weak transcription	Fetal Thymus	thymus
33	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
34	chr3:98483800-98485400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:98483800-98487200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:98483800-98487200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:98483800-98487600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:98483800-98496400	Weak transcription	Fetal Lung	lung
39	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:98484000-98485400	Enhancers	Primary hematopoietic stem cells	blood
41	chr3:98484000-98485400	Weak transcription	Left Ventricle	heart
42	chr3:98484000-98485800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:98484000-98486000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:98484000-98487200	Weak transcription	Liver	Liver
45	chr3:98484000-98488200	Weak transcription	GM12878-XiMat	blood
46	chr3:98484000-98489000	Weak transcription	Placenta	Placenta
47	chr3:98484000-98489200	Weak transcription	Psoas Muscle	Psoas
48	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:98484200-98484800	Enhancers	Primary B cells from cord blood	blood

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