Variant report

Variant	rs3862893
Chromosome Location	chr1:77836949-77836950
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	NFIC	chr1:77836147-77837316	SK-N-SH	brain:	n/a	chr1:77836324-77836340
2	JUND	chr1:77836366-77837470	SK-N-SH	brain:	n/a	n/a
3	EP300	chr1:77836202-77837142	SK-N-SH	brain:	n/a	chr1:77836438-77836454
4	RXRA	chr1:77836326-77837140	SK-N-SH	brain:	n/a	n/a
5	TEAD4	chr1:77836229-77837216	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr1:77836085-77837496	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr1:77836337-77837023	SK-N-SH_RA	brain:	n/a	n/a
8	MAX	chr1:77836618-77836996	NB4	blood:	n/a	n/a
9	JUND	chr1:77836231-77837224	SK-N-SH	brain:	n/a	n/a
10	MAFK	chr1:77836323-77837020	IMR90	lung:	n/a	n/a
11	RAD21	chr1:77836498-77836957	SK-N-SH_RA	brain:	n/a	n/a
12	POLR2A	chr1:77836910-77836990	ProgFib	skin:	n/a	n/a
13	REST	chr1:77836758-77837061	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr1:77836217-77837526	SK-N-SH	brain:	n/a	chr1:77837163-77837171 chr1:77837404-77837414 chr1:77837404-77837413 chr1:77837403-77837415 chr1:77837406-77837413 chr1:77837399-77837420 chr1:77837401-77837417
15	EP300	chr1:77836420-77837040	SK-N-SH_RA	brain:	n/a	chr1:77836438-77836454
16	USF1	chr1:77836564-77837112	SK-N-SH	brain:	n/a	n/a
17	NFIC	chr1:77836250-77837086	SK-N-SH	brain:	n/a	chr1:77836324-77836340
18	TEAD4	chr1:77836255-77837129	SK-N-SH	brain:	n/a	n/a
19	EP300	chr1:77836332-77837093	SK-N-SH	brain:	n/a	chr1:77836438-77836454
20	CEBPB	chr1:77836534-77837349	IMR90	lung:	n/a	chr1:77837107-77837119
21	USF1	chr1:77836654-77837007	SK-N-SH_RA	brain:	n/a	n/a
22	USF1	chr1:77836732-77836999	SK-N-SH_RA	brain:	n/a	n/a
23	PBX3	chr1:77836250-77837465	SK-N-SH	brain:	n/a	n/a
24	FOSL2	chr1:77836360-77837490	SK-N-SH	brain:	n/a	n/a
25	MAX	chr1:77836328-77837046	SK-N-SH	brain:	n/a	n/a
26	EP300	chr1:77836430-77837028	SK-N-SH_RA	brain:	n/a	chr1:77836438-77836454
27	POLR2A	chr1:77836461-77837059	SK-N-SH	brain:	n/a	n/a
28	SIN3AK20	chr1:77836385-77837010	SK-N-SH	brain:	n/a	n/a
29	REST	chr1:77836643-77836991	SK-N-SH	brain:	n/a	n/a
30	TCF12	chr1:77836114-77837182	SK-N-SH	brain:	n/a	n/a
31	MAX	chr1:77836250-77837074	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr1:77836644-77836957	U87	brain:	n/a	n/a
33	GATA3	chr1:77836257-77837264	SK-N-SH	brain:	n/a	chr1:77837163-77837171
34	PBX3	chr1:77836269-77837542	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
AK5	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10873935	0.86[ASN][1000 genomes]
rs11162325	0.90[ASN][1000 genomes]
rs11162326	1.00[ASN][1000 genomes]
rs11162327	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162329	0.86[ASN][1000 genomes]
rs11585455	0.88[ASN][1000 genomes]
rs12043793	0.86[ASN][1000 genomes]
rs12565526	0.88[ASN][1000 genomes]
rs1470898	0.87[ASN][1000 genomes]
rs2198511	0.95[ASN][1000 genomes]
rs2602936	0.83[ASN][1000 genomes]
rs2602937	0.96[ASN][1000 genomes]
rs2815307	0.85[ASN][1000 genomes]
rs28701620	1.00[ASN][1000 genomes]
rs6704312	0.96[ASN][1000 genomes]
rs7546116	0.82[ASN][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	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv2764210	chr1:77825478-77838400	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 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	chr1:77803400-77839200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:77834000-77839800	Enhancers	NHDF-Ad	bronchial
3	chr1:77834200-77839000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:77835200-77837200	Enhancers	Brain Cingulate Gyrus	brain
5	chr1:77835200-77838000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:77835600-77837000	Enhancers	HSMMtube	muscle
7	chr1:77835600-77837200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:77835600-77837400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr1:77835600-77837400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:77835600-77837400	Enhancers	NH-A	brain
11	chr1:77835600-77838000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr1:77835800-77837000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:77835800-77837000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:77835800-77837200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:77835800-77837200	Enhancers	Fetal Stomach	stomach
16	chr1:77835800-77837400	Enhancers	HMEC	breast
17	chr1:77835800-77846400	Weak transcription	Aorta	Aorta
18	chr1:77836000-77837000	Weak transcription	Brain Angular Gyrus	brain
19	chr1:77836000-77837000	Enhancers	HSMM	muscle
20	chr1:77836000-77837400	Enhancers	Brain Hippocampus Middle	brain
21	chr1:77836000-77837800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:77836000-77837800	Enhancers	Osteobl	bone
23	chr1:77836400-77837000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:77836400-77837000	Enhancers	Brain Anterior Caudate	brain
25	chr1:77836400-77837200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:77836400-77837200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:77836400-77837400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:77836400-77837400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:77836400-77837800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:77836400-77838000	Enhancers	Primary T cells from cord blood	blood
31	chr1:77836400-77838000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr1:77836400-77838400	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:77836600-77837000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr1:77836600-77837000	Enhancers	Brain Substantia Nigra	brain
35	chr1:77836600-77837000	Active TSS	NHLF	lung
36	chr1:77836600-77837200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:77836600-77837200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:77836600-77837400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:77836600-77837400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:77836600-77837400	Enhancers	NHEK	skin
41	chr1:77836600-77840800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:77836600-77844000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:77836600-77844400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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