Variant report

Variant	rs12717801
Chromosome Location	chr1:95549317-95549318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:95549239..95551783-chr1:95557722..95560296,2	K562	blood:
2	chr1:95538304..95542687-chr1:95547314..95551412,4	K562	blood:
3	chr1:95548633..95550280-chr1:95551848..95554407,2	K562	blood:
4	chr1:95548534..95550560-chr1:95561242..95563243,2	K562	blood:
5	chr1:95537906..95540318-chr1:95548748..95550282,2	MCF-7	breast:
6	chr1:95543478..95545914-chr1:95548996..95550848,2	K562	blood:
7	chr1:95545358..95548450-chr1:95548611..95551467,3	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALG14-6	chr1:95549078-95549337	l_92_chr1:95549077-95556423_testes
2	lnc-ALG14-6	chr1:95549072-95549337	NONHSAT004641

No data

Variant related genes	Relation type
ENSG00000172339	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10127516	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874901	0.84[JPT][hapmap]
rs10874903	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165285	0.84[JPT][hapmap]
rs11576940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810584	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];1.00[ASN][1000 genomes]
rs12562498	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563154	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12724815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3890845	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4309031	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4314930	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4335417	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4427415	0.88[JPT][hapmap]
rs4556411	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4623755	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950059	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];1.00[ASN][1000 genomes]
rs4950070	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593667	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593670	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6669249	0.94[JPT][hapmap]
rs6690421	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512953	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541757	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546710	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9437816	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 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	chr1:95542000-95549600	Weak transcription	HepG2	liver
2	chr1:95546400-95550600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:95546600-95550400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:95546600-95552000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:95546800-95550400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:95546800-95550400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:95546800-95550600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:95549000-95549800	Enhancers	K562	blood
9	chr1:95549000-95551200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr1:95549200-95549800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:95549200-95550400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:95549200-95552400	Enhancers	A549	lung
13	chr1:95549200-95554200	Enhancers	Fetal Heart	heart

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