Variant report

Variant	rs12665399
Chromosome Location	chr6:140290885-140290886
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:140289780..140291502-chr6:140292596..140295071,2	K562	blood:
2	chr6:140289417..140292711-chr6:140293441..140296166,4	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1028469	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10434888	0.95[CEU][hapmap]
rs10872525	0.95[CEU][hapmap]
rs12175776	0.82[EUR][1000 genomes]
rs12525047	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12526885	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12663217	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12663483	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13191189	0.88[CEU][hapmap]
rs13194747	0.87[EUR][1000 genomes]
rs13194827	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1416289	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069768	0.95[CEU][hapmap]
rs1933742	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1953788	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1953789	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs586246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs587235	0.90[CHB][hapmap];0.82[JPT][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs592056	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs598498	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs616279	0.90[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs618515	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs622216	0.96[ASN][1000 genomes]
rs62429515	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62429516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62429517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs647968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs648510	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs650774	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs67013338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs679849	0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs680290	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs681235	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6926807	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6928433	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724061	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743656	0.88[ASN][1000 genomes]
rs7758187	0.95[CEU][hapmap]
rs856646	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9373255	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373256	0.95[CEU][hapmap]
rs9373259	1.00[CEU][hapmap]
rs9376482	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9376485	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9376494	0.95[CEU][hapmap]
rs9385888	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9385895	0.95[CEU][hapmap]
rs9385901	0.82[CEU][hapmap]
rs9385902	0.95[CEU][hapmap]
rs9389733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9389741	0.95[CEU][hapmap]
rs9399298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9399299	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399304	0.90[CEU][hapmap]
rs9399308	1.00[CEU][hapmap]
rs9403134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403135	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9403148	0.95[CEU][hapmap]
rs9495636	0.90[YRI][hapmap]
rs9495641	0.90[YRI][hapmap]

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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140284400-140292200	Weak transcription	Placenta	Placenta
2	chr6:140286800-140291400	Weak transcription	NH-A	brain
3	chr6:140287000-140292600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:140287800-140299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:140289200-140291600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:140289200-140291600	Weak transcription	NHDF-Ad	bronchial
7	chr6:140289200-140291600	Weak transcription	Osteobl	bone
8	chr6:140289200-140292400	Weak transcription	HSMM	muscle
9	chr6:140289200-140294400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:140289400-140294800	Weak transcription	HUVEC	blood vessel
11	chr6:140289600-140297200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:140290000-140291400	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links