Variant report

Variant	rs12124322
Chromosome Location	chr1:227612230-227612231
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12025219	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12118780	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs12125212	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12125342	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129915	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132916	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738593	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12745048	0.85[JPT][hapmap]
rs4601553	0.83[CHB][hapmap];0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1003278	chr1:227563126-227678464	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv873243	chr1:227581017-227617519	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12124322	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227606200-227612400	Weak transcription	Left Ventricle	heart
2	chr1:227610600-227615200	Weak transcription	K562	blood
3	chr1:227611600-227612400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:227611800-227612400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:227611800-227612600	Enhancers	Small Intestine	intestine
6	chr1:227611800-227612800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:227611800-227612800	Enhancers	HUVEC	blood vessel
8	chr1:227611800-227613000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:227612000-227612600	Enhancers	Colon Smooth Muscle	Colon
10	chr1:227612000-227612800	Enhancers	A549	lung
11	chr1:227612000-227613000	Active TSS	Brain Substantia Nigra	brain
12	chr1:227612200-227612600	Enhancers	Sigmoid Colon	Sigmoid Colon

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Input of quick search could be:

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

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