Variant report

Variant	rs13386710
Chromosome Location	chr2:127266807-127266808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10179912	0.89[YRI][hapmap]
rs10182007	0.94[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10194561	0.90[AFR][1000 genomes]
rs10203788	0.90[AFR][1000 genomes]
rs13382980	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13413216	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13415629	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13419397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425593	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13425595	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440050	0.87[EUR][1000 genomes]
rs4577234	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56896312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6431080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6431081	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6431097	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6727953	0.92[EUR][1000 genomes]
rs7590145	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7591893	0.92[EUR][1000 genomes]
rs7598599	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7599320	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599552	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604896	0.82[EUR][1000 genomes]
rs7606965	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs958916	0.83[AFR][1000 genomes]
rs961447	0.86[AFR][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	nsv1001995	chr2:126506739-127314488	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1002265	chr2:127029745-127733458	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv535919	chr2:127029745-127733458	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv834364	chr2:127100752-127267070	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13386710	ITGAD	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127265200-127267400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:127265200-127268400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:127265200-127270000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:127265400-127268000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:127265400-127270600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:127265600-127267800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:127265800-127267200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:127265800-127267200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:127266600-127267600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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