Variant report

Variant	rs2473623
Chromosome Location	chr1:210659966-210659967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11582700	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12408469	0.84[ASN][1000 genomes]
rs12411254	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs12728693	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap]
rs12759944	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs17188260	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs17260445	1.00[YRI][hapmap]
rs4348724	0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs4500315	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4622068	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs4845035	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs6691136	1.00[YRI][hapmap]
rs7544655	0.83[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	nsv4376	chr1:210627620-210672326	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv275540	chr1:210658336-210663000	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2473623	LOC642587	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210639400-210668200	Weak transcription	Primary T cells from cord blood	blood
2	chr1:210640000-210660400	Weak transcription	Aorta	Aorta
3	chr1:210643200-210674000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:210648800-210660400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:210653800-210678800	Weak transcription	HSMM	muscle
6	chr1:210657000-210660400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:210657000-210663600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:210657000-210669600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:210658000-210660200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:210658800-210663000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:210658800-210664800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:210659000-210663600	Strong transcription	HSMMtube	muscle
13	chr1:210659800-210661600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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