Variant report

Variant	rs6689231
Chromosome Location	chr1:171903507-171903508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1022541	0.90[EUR][1000 genomes]
rs1040517	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs10737338	0.84[EUR][1000 genomes]
rs10753202	0.86[EUR][1000 genomes]
rs10753203	0.86[EUR][1000 genomes]
rs10753204	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs10798705	0.86[EUR][1000 genomes]
rs10798722	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs10798725	0.86[EUR][1000 genomes]
rs10798726	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs10913908	0.86[EUR][1000 genomes]
rs12021814	0.90[EUR][1000 genomes]
rs12024869	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12025243	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12029015	0.87[CHB][hapmap];0.84[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12040254	0.91[CEU][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12047542	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12747663	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1535301	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs1555100	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs1972340	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1980488	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2145383	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34906981	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4596936	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916235	0.87[EUR][1000 genomes]
rs4916400	0.83[EUR][1000 genomes]
rs4916401	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs4916404	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs4916411	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425456	0.86[EUR][1000 genomes]
rs6425468	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs6425484	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6425518	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6660011	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs6665335	0.87[EUR][1000 genomes]
rs6673646	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs6679341	0.88[EUR][1000 genomes]
rs6686260	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs6690848	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs71523161	0.91[EUR][1000 genomes]
rs7517331	0.83[EUR][1000 genomes]
rs7526653	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs7554700	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs7554935	0.88[EUR][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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171879800-171908000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:171899800-171905200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:171900000-171916200	Weak transcription	Lung	lung
4	chr1:171900200-171905800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:171900400-171903600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:171901800-171904000	Enhancers	Brain Substantia Nigra	brain
7	chr1:171902600-171903800	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr1:171903000-171904600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:171903000-171909000	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:171903200-171905600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:171903200-171908600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:171903200-171908600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:171903200-171909000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:171903400-171903600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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