Variant report

Variant	rs1708681
Chromosome Location	chr4:89965459-89965460
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:89958290..89961976-chr4:89962319..89966068,4	K562	blood:
2	chr4:89958647..89961976-chr4:89962746..89966068,3	K562	blood:
3	chr4:89965401..89967531-chr4:89976888..89979079,2	K562	blood:
4	chr4:89965264..89968195-chr4:89977479..89979113,3	K562	blood:
5	chr4:89963957..89965462-chr4:89973010..89975706,2	K562	blood:

Variant related genes	Relation type
ENSG00000138640	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10004888	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10006121	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10009019	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10025142	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10028596	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10030965	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10033484	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10470937	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11097206	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11097208	0.91[ASN][1000 genomes]
rs11737016	0.85[ASN][1000 genomes]
rs11737182	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11935610	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12512799	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12640018	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12645240	0.84[ASN][1000 genomes]
rs13148188	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1398940	0.96[ASN][1000 genomes]
rs1458557	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16996143	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17015027	0.87[ASN][1000 genomes]
rs1708668	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1708669	0.94[ASN][1000 genomes]
rs1708670	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1795722	0.94[ASN][1000 genomes]
rs1795727	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1795729	0.97[ASN][1000 genomes]
rs1795734	0.96[ASN][1000 genomes]
rs1795738	0.93[ASN][1000 genomes]
rs1849597	0.96[ASN][1000 genomes]
rs1903006	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1903007	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1921679	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1921683	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1921684	0.92[ASN][1000 genomes]
rs1961979	0.92[ASN][1000 genomes]
rs2018779	0.82[ASN][1000 genomes]
rs2085601	0.85[ASN][1000 genomes]
rs2090031	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2178583	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2178584	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2178585	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2464514	0.94[ASN][1000 genomes]
rs2609275	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2670623	0.93[ASN][1000 genomes]
rs2704571	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704573	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2704574	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704576	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704577	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704596	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28540701	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28600923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2869969	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2869971	0.92[ASN][1000 genomes]
rs2869972	0.92[ASN][1000 genomes]
rs2869973	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28712360	0.91[ASN][1000 genomes]
rs2904261	0.92[ASN][1000 genomes]
rs34749134	0.82[ASN][1000 genomes]
rs34869341	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35232147	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35441198	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4285052	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4437212	0.84[AMR][1000 genomes]
rs4450885	0.91[ASN][1000 genomes]
rs4507326	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4693981	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60618725	0.85[ASN][1000 genomes]
rs62306363	0.90[ASN][1000 genomes]
rs62306364	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62306390	0.86[ASN][1000 genomes]
rs62306391	0.85[ASN][1000 genomes]
rs6532091	0.82[ASN][1000 genomes]
rs6815703	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6819725	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6827857	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6834787	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6844655	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6852373	0.96[ASN][1000 genomes]
rs6852947	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72877642	0.85[ASN][1000 genomes]
rs7654714	0.84[AMR][1000 genomes]
rs7656238	0.92[ASN][1000 genomes]
rs7659904	0.91[ASN][1000 genomes]
rs7660314	0.91[ASN][1000 genomes]
rs7680864	0.91[ASN][1000 genomes]
rs7686954	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7692455	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7697075	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7697900	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7697921	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9307053	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9307054	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9307055	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9307060	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9307061	0.91[ASN][1000 genomes]
rs9991237	0.91[ASN][1000 genomes]
rs9991800	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9995465	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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89937200-89975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
3	chr4:89946200-89972800	Weak transcription	A549	lung
4	chr4:89958000-89972200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:89958200-89974400	Weak transcription	Aorta	Aorta
6	chr4:89958400-89965600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:89958400-89970200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:89958400-89971400	Weak transcription	Ovary	ovary
9	chr4:89959000-89972200	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:89959000-89972400	Weak transcription	Fetal Intestine Small	intestine
11	chr4:89959000-89972600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:89959000-89975400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:89959200-89974400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:89959400-89972200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:89962000-89971200	Weak transcription	K562	blood
16	chr4:89963200-89975800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:89965400-89966000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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