Variant report

Variant	rs12693546
Chromosome Location	chr2:190486357-190486358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10170389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693544	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010391	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391190	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404407	0.80[CHB][hapmap]
rs1437887	0.85[YRI][hapmap]
rs16831652	0.90[CHB][hapmap]
rs17271204	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35358917	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6434349	0.90[CHB][hapmap]
rs6735087	0.84[YRI][hapmap]
rs7587662	0.85[YRI][hapmap]
rs7604386	0.92[CEU][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7604627	0.90[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12693546	SLC40A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190479000-190503800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:190484000-190490600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:190484400-190489400	Weak transcription	HepG2	liver
4	chr2:190484400-190493800	Weak transcription	A549	lung
5	chr2:190484600-190494400	Weak transcription	HUVEC	blood vessel
6	chr2:190485600-190489400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:190485800-190489000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:190485800-190489000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:190486200-190494400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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