Variant report

Variant	rs1860604
Chromosome Location	chr12:42298132-42298133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10491997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181236	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181237	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11181239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181240	0.96[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12310489	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1234008	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1497168	0.84[EUR][1000 genomes]
rs1860605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406427	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs722216	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305744	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7308779	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7309314	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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	nsv899043	chr12:42058138-42313665	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv899044	chr12:42058138-42321161	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42294800-42301000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:42295200-42299200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr12:42295800-42299800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:42297200-42301200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr12:42297600-42298400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:42297600-42300800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:42297600-42300800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:42297800-42299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:42297800-42300000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:42298000-42298200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr12:42298000-42298200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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