Variant report

Variant	rs11057375
Chromosome Location	chr12:124346336-124346337
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10773040	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs10773042	0.99[ASN][1000 genomes]
rs10773043	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10846561	0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.80[ASN][1000 genomes]
rs10846563	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10846564	0.88[GIH][hapmap]
rs10846565	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10846566	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs10846568	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11057374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057378	0.92[ASN][1000 genomes]
rs11057379	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap]
rs11057380	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11057385	0.86[ASN][1000 genomes]
rs12228611	0.95[ASN][1000 genomes]
rs1882488	1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1922257	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.98[ASN][1000 genomes]
rs2341779	0.90[GIH][hapmap]
rs7138100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7300162	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7314963	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.95[YRI][hapmap];0.98[ASN][1000 genomes]
rs7959043	0.95[ASN][1000 genomes]
rs7960854	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7961179	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7962016	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980570	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11057375	TMEM120B	cis	parietal	SCAN
rs11057375	P2RX4	cis	cerebellum	SCAN
rs11057375	B3GNT4	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124331400-124352800	Weak transcription	Fetal Brain Female	brain
2	chr12:124342400-124346600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:124343400-124347800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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