Variant report

Variant	rs2802683
Chromosome Location	chr6:69398622-69398623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:69398238..69400997-chr6:69423873..69426595,2	K562	blood:
2	chr6:69397594..69401591-chr6:69402170..69406294,3	K562	blood:
3	chr6:69384897..69387338-chr6:69398147..69399804,2	K562	blood:
4	chr6:69396018..69398717-chr6:69401123..69403909,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL713998.1-7	chr6:69397184-69399669	l_3201_chr6:69396542-69401446_brain

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1033520	0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10455676	0.80[ASN][1000 genomes]
rs10484791	0.84[CEU][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs10945138	0.96[CEU][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10945139	0.82[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs10945141	0.82[JPT][hapmap]
rs10945142	0.80[JPT][hapmap]
rs11752398	0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11752837	0.82[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12154008	0.82[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs12192235	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12200101	0.86[EUR][1000 genomes]
rs12201488	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12206940	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12210045	0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12214149	0.80[JPT][hapmap]
rs13218712	0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2246104	0.86[JPT][hapmap]
rs2253759	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2253866	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2254654	0.96[CEU][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2585592	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2585597	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2585598	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2585599	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2585600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2585604	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2585621	0.82[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2585622	0.81[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2585623	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2585626	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2585627	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2746125	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2746127	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2746130	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2746131	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2746132	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2746134	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2746135	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2746137	0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2746140	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746141	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2802676	0.96[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2802677	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2802680	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802684	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802687	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2802688	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2802689	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2802691	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2802693	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2802694	0.93[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2802701	0.81[JPT][hapmap]
rs3121775	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6931354	0.82[JPT][hapmap]
rs715294	0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7745837	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7768591	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9360356	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1015906	chr6:69376236-69416331	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69352200-69399000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:69364200-69399800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:69379200-69398800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:69383200-69400000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:69388400-69399800	Weak transcription	Fetal Lung	lung
6	chr6:69389600-69399800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:69393400-69399800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:69396600-69398800	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:69396600-69399800	Weak transcription	Brain Angular Gyrus	brain
10	chr6:69396600-69399800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:69396600-69399800	Weak transcription	Brain Substantia Nigra	brain
12	chr6:69397400-69398800	Enhancers	K562	blood
13	chr6:69398600-69398800	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links