Variant report

Variant	rs12474853
Chromosome Location	chr2:72268539-72268540
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10204373	0.83[ASN][1000 genomes]
rs34243964	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35667135	0.97[ASN][1000 genomes]
rs4852278	0.96[ASN][1000 genomes]
rs4852279	0.97[ASN][1000 genomes]
rs741161	0.83[ASN][1000 genomes]

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	nsv874261	chr2:72242013-72270790	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv874262	chr2:72242013-72279514	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv3584760	chr2:72249991-72271489	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv874263	chr2:72251751-72279514	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12474853	GFPT1	cis	cerebellum	SCAN
rs12474853	TACR1	cis	parietal	SCAN
rs12474853	FBXO48	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72266000-72270200	Enhancers	Esophagus	oesophagus
2	chr2:72266600-72268600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:72266800-72268600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:72267600-72269600	Enhancers	HMEC	breast
5	chr2:72267800-72269000	Enhancers	Spleen	Spleen
6	chr2:72267800-72269200	Flanking Active TSS	NHEK	skin
7	chr2:72267800-72269600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:72268000-72269000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:72268200-72268600	Enhancers	Osteobl	bone
10	chr2:72268200-72268800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:72268200-72269600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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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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