Variant report

Variant	rs4951960
Chromosome Location	chr2:31251499-31251500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10197865	0.80[MEX][hapmap]
rs10198054	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10209881	0.92[MEX][hapmap]
rs10865086	0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs12464083	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12613732	0.93[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12617279	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs12621546	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12712300	0.82[GIH][hapmap];0.92[MEX][hapmap]
rs12712301	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12712304	0.87[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs12999804	0.82[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1862966	0.81[ASW][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs1862967	0.81[ASW][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs1862968	0.81[ASW][hapmap];0.80[GIH][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs2194455	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4245766	0.80[CHD][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs4952031	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs5009910	0.81[ASW][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs6752303	0.87[MEX][hapmap]
rs7558425	0.82[AMR][1000 genomes]
rs7605643	0.82[GIH][hapmap];0.92[MEX][hapmap]
rs7605982	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608731	0.87[MEX][hapmap]
rs9679162	0.80[MEX][hapmap]

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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4951960	GALNT14	cis	parietal	SCAN
rs4951960	SLC30A6	cis	cerebellum	SCAN
rs4951960	PLLP	trans	cerebellum	SCAN
rs4951960	FAM179A	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31246400-31261600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:31250200-31254200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:31250400-31252000	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr2:31250800-31251800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:31250800-31251800	Enhancers	Brain Germinal Matrix	brain
6	chr2:31250800-31252000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:31250800-31252200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr2:31251000-31251800	Enhancers	H9 Cell Line	embryonic stem cell
9	chr2:31251000-31251800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr2:31251000-31251800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:31251000-31251800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:31251000-31252000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr2:31251400-31251800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:31251400-31270000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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