Variant report

Variant	rs1865863
Chromosome Location	chr3:78803784-78803785
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	TCF12	chr3:78803047-78803815	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr3:78803760-78803822	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000240752	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10049014	0.89[CEU][hapmap]
rs10049102	0.80[CEU][hapmap]
rs10428105	0.89[CEU][hapmap]
rs11914618	0.90[CEU][hapmap]
rs11920344	0.90[CEU][hapmap]
rs11923155	0.82[ASN][1000 genomes]
rs11925970	0.81[CEU][hapmap]
rs11928868	0.90[CEU][hapmap]
rs1395784	0.94[CEU][hapmap]
rs1457659	0.81[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs1487135	0.80[CHB][hapmap]
rs162425	0.84[CHB][hapmap]
rs162428	0.81[CHB][hapmap]
rs162429	0.80[CHB][hapmap]
rs17016466	0.90[CEU][hapmap]
rs17311036	0.83[ASN][1000 genomes]
rs17311057	0.83[ASN][1000 genomes]
rs17311169	0.89[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs17375110	0.90[CEU][hapmap]
rs17375496	0.90[CEU][hapmap]
rs17375739	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs17376753	0.83[ASN][1000 genomes]
rs1825760	0.80[CHB][hapmap]
rs1865860	0.95[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1865861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961636	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018432	0.80[CHB][hapmap]
rs2082973	0.80[CHB][hapmap]
rs2271151	0.90[CEU][hapmap]
rs329805	0.81[CHB][hapmap]
rs329819	0.80[CHB][hapmap]
rs333483	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs333506	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs333507	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs35077320	0.88[ASN][1000 genomes]
rs3732663	0.90[CEU][hapmap]
rs3773226	0.90[CEU][hapmap]
rs3773231	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs3773234	0.90[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773239	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773240	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773245	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821601	0.90[CEU][hapmap]
rs3821602	0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821603	0.90[CEU][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4263256	0.90[CEU][hapmap]
rs4681013	0.94[JPT][hapmap]
rs531125	0.80[CHB][hapmap]
rs56077922	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57046576	0.88[ASN][1000 genomes]
rs58423115	0.89[EUR][1000 genomes]
rs58792018	0.83[ASN][1000 genomes]
rs59263997	0.88[ASN][1000 genomes]
rs61053911	0.81[EUR][1000 genomes]
rs6548595	0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66496525	0.88[ASN][1000 genomes]
rs66528054	0.88[ASN][1000 genomes]
rs67488304	0.82[ASN][1000 genomes]
rs6769933	0.89[CEU][hapmap]
rs67703869	0.88[ASN][1000 genomes]
rs6787349	0.81[CEU][hapmap]
rs6788434	0.90[CEU][hapmap]
rs6788511	0.81[CEU][hapmap]
rs72892461	0.88[ASN][1000 genomes]
rs72892501	0.83[ASN][1000 genomes]
rs73109772	0.88[EUR][1000 genomes]
rs73109774	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73113488	0.87[ASN][1000 genomes]
rs73848602	0.83[ASN][1000 genomes]
rs7610686	0.90[CEU][hapmap]
rs7610996	0.80[CHB][hapmap]
rs7613490	0.89[CEU][hapmap]
rs7616495	0.90[CEU][hapmap]
rs7622194	0.90[CEU][hapmap]
rs7624482	0.80[CEU][hapmap]
rs7650002	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7653782	0.85[CEU][hapmap]
rs767182	0.90[CEU][hapmap]
rs9808950	0.81[CEU][hapmap]
rs9819398	0.83[CEU][hapmap]
rs9823359	0.90[CEU][hapmap]
rs9861603	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9866912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9880072	0.90[CEU][hapmap]
rs9880316	0.81[CEU][hapmap]
rs9882811	0.90[CEU][hapmap]
rs997274	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2753211	chr3:78784269-78809116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78787400-78814800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:78798600-78810200	Weak transcription	Fetal Lung	lung
3	chr3:78801800-78804000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:78802200-78810200	Weak transcription	Fetal Stomach	stomach
5	chr3:78802400-78803800	Enhancers	Brain Anterior Caudate	brain
6	chr3:78802400-78804000	Enhancers	Brain Substantia Nigra	brain
7	chr3:78802400-78804200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:78802400-78804200	Enhancers	HMEC	breast
9	chr3:78802400-78804400	Enhancers	Hela-S3	cervix
10	chr3:78802400-78804600	Enhancers	Brain Angular Gyrus	brain
11	chr3:78802600-78803800	Enhancers	NH-A	brain
12	chr3:78802600-78804000	Enhancers	Osteobl	bone
13	chr3:78802600-78804200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:78802600-78804600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:78802800-78803800	Enhancers	NHLF	lung
16	chr3:78802800-78804000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:78802800-78804000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:78802800-78804000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:78802800-78804200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr3:78803000-78804000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:78803000-78804000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:78803000-78804000	Weak transcription	Pancreas	Pancrea
23	chr3:78803200-78803800	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr3:78803200-78803800	Enhancers	NHEK	skin
25	chr3:78803200-78804200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:78803200-78804600	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:78803200-78804800	Enhancers	HepG2	liver
28	chr3:78803400-78803800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:78803400-78803800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:78803400-78803800	Enhancers	Brain Germinal Matrix	brain
31	chr3:78803400-78803800	Enhancers	Colon Smooth Muscle	Colon
32	chr3:78803400-78803800	Enhancers	Fetal Brain Female	brain
33	chr3:78803400-78803800	Enhancers	NHDF-Ad	bronchial
34	chr3:78803400-78804600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr3:78803400-78804600	Enhancers	Fetal Muscle Leg	muscle
36	chr3:78803400-78806600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:78803600-78804000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:78803600-78804000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:78803600-78804600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr3:78803600-78805800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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