Variant report

Variant	rs6695554
Chromosome Location	chr1:67230205-67230206
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	chr1:67229958..67230621-chr1:67677554..67678086,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10493416	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493417	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493418	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493419	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10493420	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060575	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208952	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs11208953	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063724	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070460	0.87[ASN][1000 genomes]
rs12727390	1.00[ASN][1000 genomes]
rs12727422	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12733829	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17441669	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442177	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442361	0.93[ASN][1000 genomes]
rs1812444	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1909184	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270702	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34089513	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36100970	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816989	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56336376	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696874	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697073	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699313	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68045184	1.00[ASN][1000 genomes]
rs68063507	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515248	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7519784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525761	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535868	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545934	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv830093	chr1:67173594-67348264	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1009176	chr1:67227876-67231940	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6695554	TCTEX1D1	cis	parietal	SCAN
rs6695554	DLEU2L	cis	parietal	SCAN
rs6695554	ANGPTL3	cis	parietal	SCAN
rs6695554	SGIP1	cis	parietal	SCAN
rs6695554	TCTEX1D1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67221600-67236400	Weak transcription	Liver	Liver
2	chr1:67222800-67236200	Weak transcription	Psoas Muscle	Psoas
3	chr1:67226200-67231400	Weak transcription	K562	blood
4	chr1:67227400-67236400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:67228600-67230800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:67229400-67236400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:67229800-67236200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:67230200-67230400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:67230200-67231600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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