Variant report

Variant	rs12002124
Chromosome Location	chr9:103161860-103161861
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103114953..103119242-chr9:103160329..103162600,3	K562	blood:
2	chr9:103139380..103141850-chr9:103159485..103162219,2	K562	blood:

Variant related genes	Relation type
ENSG00000136891	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10819755	0.86[CEU][hapmap]
rs10819758	0.91[CEU][hapmap];0.90[GIH][hapmap]
rs10819771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989046	0.82[CEU][hapmap]
rs10989047	0.91[CEU][hapmap]
rs10989051	0.91[CEU][hapmap];0.90[GIH][hapmap]
rs10989072	0.91[CEU][hapmap];0.90[GIH][hapmap]
rs10989073	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989075	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989077	0.90[EUR][1000 genomes]
rs11790431	0.82[CEU][hapmap];0.90[GIH][hapmap]
rs11791943	0.91[YRI][hapmap]
rs12000794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375859	0.87[EUR][1000 genomes]
rs12378432	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13284601	1.00[CHB][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919024	0.82[CEU][hapmap];0.90[GIH][hapmap]
rs2039396	1.00[ASN][1000 genomes]
rs2039397	1.00[ASN][1000 genomes]
rs5018733	1.00[LWK][hapmap]
rs7027939	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029342	0.89[CEU][hapmap]
rs7039994	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs7849019	0.91[CEU][hapmap]
rs944942	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12002124	CYLC2	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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