Variant report

Variant	rs7417186
Chromosome Location	chr1:95546430-95546431
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95544414..95547978-chr1:95549348..95553409,4	K562	blood:
2	chr1:95545358..95548450-chr1:95548611..95551467,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10465759	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.95[ASN][1000 genomes]
rs11165297	0.86[JPT][hapmap]
rs11590106	0.86[JPT][hapmap]
rs11801110	0.86[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12129041	0.80[JPT][hapmap]
rs12239887	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12751633	0.86[JPT][hapmap]
rs12755096	0.86[JPT][hapmap]
rs12760863	0.86[JPT][hapmap]
rs17112857	0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2391390	0.86[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs34726676	0.95[ASN][1000 genomes]
rs34850224	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34923964	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35578830	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3890785	0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4131811	0.86[JPT][hapmap]
rs4300274	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4387224	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4540701	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4615892	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55902261	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55911502	0.94[ASN][1000 genomes]
rs60846886	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6662345	0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.81[MKK][hapmap];0.98[ASN][1000 genomes]
rs6672635	0.98[ASN][1000 genomes]
rs6674467	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674604	0.86[JPT][hapmap]
rs6678809	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6679106	0.86[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs6680551	0.81[ASW][hapmap];0.97[LWK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs6684137	0.93[ASW][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687351	0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.81[MKK][hapmap];0.98[ASN][1000 genomes]
rs6689195	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6697256	0.88[TSI][hapmap]
rs6704022	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs71654403	0.95[ASN][1000 genomes]
rs71654404	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71654405	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71654406	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71654407	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71654408	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7540821	0.86[JPT][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7417186	SLC44A3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95539800-95549000	Weak transcription	K562	blood
2	chr1:95542000-95549600	Weak transcription	HepG2	liver
3	chr1:95546000-95546600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr1:95546000-95546600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:95546000-95546600	Enhancers	Brain Cingulate Gyrus	brain
6	chr1:95546000-95546800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:95546000-95546800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr1:95546000-95546800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:95546000-95546800	Enhancers	Brain Angular Gyrus	brain
10	chr1:95546000-95546800	Enhancers	Brain Hippocampus Middle	brain
11	chr1:95546200-95546600	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr1:95546200-95546800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr1:95546400-95550600	Weak transcription	H1 Cell Line	embryonic stem cell

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