Variant report

Variant	rs10873966
Chromosome Location	chr1:78638316-78638317
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	GATA3	chr1:78637322-78638419	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr1:78637241-78638495	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr1:78637327-78638503	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:78637729-78638369	U87	brain:	n/a	n/a
5	GATA3	chr1:78637250-78638555	SK-N-SH	brain:	n/a	n/a
6	EP300	chr1:78637247-78638507	SK-N-SH	brain:	n/a	n/a
7	FOSL2	chr1:78637380-78638417	SK-N-SH	brain:	n/a	n/a
8	JUND	chr1:78637305-78638473	SK-N-SH	brain:	n/a	n/a
9	GATA2	chr1:78637473-78638327	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
RNFT1P2	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1022103	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11162415	0.94[ASN][1000 genomes]
rs11162417	0.89[ASN][1000 genomes]
rs11162418	0.84[EUR][1000 genomes]
rs11162425	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162429	0.99[ASN][1000 genomes]
rs11579434	0.94[ASN][1000 genomes]
rs12083265	0.84[EUR][1000 genomes]
rs12095545	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131414	0.84[EUR][1000 genomes]
rs12184300	1.00[ASN][1000 genomes]
rs12749252	0.84[EUR][1000 genomes]
rs12758374	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1323094	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1359043	0.84[EUR][1000 genomes]
rs1621088	0.84[EUR][1000 genomes]
rs1770306	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1770313	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1890850	0.99[ASN][1000 genomes]
rs2025610	0.84[EUR][1000 genomes]
rs2025611	0.85[EUR][1000 genomes]
rs2146612	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2208966	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209472	0.83[EUR][1000 genomes]
rs2351907	0.81[EUR][1000 genomes]
rs2351909	0.84[EUR][1000 genomes]
rs2351910	0.84[EUR][1000 genomes]
rs2882796	0.84[EUR][1000 genomes]
rs4258183	0.81[EUR][1000 genomes]
rs4529663	0.84[EUR][1000 genomes]
rs4587522	0.83[EUR][1000 genomes]
rs4650315	0.82[EUR][1000 genomes]
rs4650382	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4650619	0.89[ASN][1000 genomes]
rs4650620	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs581926	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58611517	0.83[EUR][1000 genomes]
rs596803	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs599386	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs600237	0.80[EUR][1000 genomes]
rs616518	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61777350	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs619749	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs627493	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs627549	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs638232	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs640124	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs649502	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs653899	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs669357	0.89[CEU][hapmap]
rs669764	0.89[CEU][hapmap]
rs671229	0.80[EUR][1000 genomes]
rs680143	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs688570	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs689374	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72688712	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7417073	0.81[EUR][1000 genomes]
rs7524877	0.94[ASN][1000 genomes]
rs7532752	0.84[EUR][1000 genomes]
rs7555504	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS 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 miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850497	chr1:78596312-78645701	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78625200-78644400	Weak transcription	Pancreas	Pancrea
2	chr1:78635000-78646200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:78636600-78638600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:78636800-78638400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:78637000-78638600	Enhancers	HSMM	muscle
6	chr1:78637200-78638400	Enhancers	Esophagus	oesophagus
7	chr1:78637200-78638600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:78637200-78638600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:78637200-78638800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:78637200-78639400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:78637400-78638400	Enhancers	NHLF	lung
12	chr1:78637600-78638600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:78637600-78638600	Enhancers	HUVEC	blood vessel
14	chr1:78637600-78638600	Enhancers	NHDF-Ad	bronchial
15	chr1:78638000-78638400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:78638000-78638400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:78638000-78638400	Enhancers	Hela-S3	cervix
18	chr1:78638000-78638600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:78638000-78638600	Enhancers	NHEK	skin
20	chr1:78638000-78638600	Enhancers	Osteobl	bone
21	chr1:78638000-78638800	Enhancers	HMEC	breast
22	chr1:78638200-78638400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:78638200-78638600	Enhancers	NH-A	brain

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