Variant report

Variant	rs864899
Chromosome Location	chr12:51221127-51221128
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10783382	0.82[CHB][hapmap]
rs10783387	0.92[CEU][hapmap]
rs10783389	0.86[CHB][hapmap]
rs10876095	0.89[CHB][hapmap]
rs10876096	0.86[CHB][hapmap]
rs10876097	0.86[CHB][hapmap]
rs10876098	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs11169532	0.82[CHB][hapmap]
rs11169544	0.81[CHB][hapmap]
rs11169552	0.86[CHB][hapmap]
rs11169560	0.86[CHB][hapmap]
rs11169561	0.86[CHB][hapmap]
rs11169567	0.92[CEU][hapmap]
rs11169571	0.92[CEU][hapmap]
rs11169578	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1129406	0.92[CEU][hapmap]
rs12372718	0.89[CEU][hapmap]
rs1344958	0.86[CHB][hapmap]
rs2554862	0.90[YRI][hapmap]
rs3742064	0.82[CHB][hapmap]
rs3809319	0.86[CHB][hapmap]
rs3825402	0.86[CHB][hapmap]
rs4307773	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs4768866	0.86[CHB][hapmap]
rs4768907	0.82[CHB][hapmap]
rs4768922	0.86[CHB][hapmap]
rs4768924	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs4768925	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs4768940	0.84[ASN][1000 genomes]
rs7133974	0.92[CEU][hapmap]
rs7306677	0.92[CEU][hapmap]
rs829112	0.90[YRI][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv899078	chr12:51213433-51286750	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs864899	CERS5	cis	Nerve Tibial	GTEx
rs864899	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs864899	ATF1	cis	Artery Tibial	GTEx
rs864899	KIAA1463	cis	multi-tissue	Pritchard
rs864899	DIP2B	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51200600-51222200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:51205000-51228200	Weak transcription	Gastric	stomach
3	chr12:51210200-51222000	Weak transcription	Esophagus	oesophagus
4	chr12:51210600-51222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:51210600-51223400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:51211000-51222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:51211000-51222000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:51213200-51222200	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:51213400-51221800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:51213400-51222600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:51213800-51222800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:51218800-51223400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:51219200-51221800	Weak transcription	HMEC	breast
14	chr12:51219200-51223000	Weak transcription	Brain Anterior Caudate	brain
15	chr12:51219400-51222400	Weak transcription	Brain Substantia Nigra	brain
16	chr12:51219600-51222200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:51219600-51222400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:51219600-51222800	Weak transcription	Thymus	Thymus
19	chr12:51220200-51222200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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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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