Variant report

Variant	rs2579550
Chromosome Location	chr2:96741944-96741945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10183151	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs1030864	0.86[EUR][1000 genomes]
rs11680950	1.00[ASW][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs11683523	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11687113	0.91[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap]
rs1168965	0.86[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168968	0.81[CEU][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1168970	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs1168972	0.86[EUR][1000 genomes]
rs1168974	1.00[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs1168975	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs1168976	1.00[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs11689832	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs11695514	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs1724125	0.84[EUR][1000 genomes]
rs2140938	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2229169	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2301707	0.81[CEU][hapmap]
rs2312955	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2438972	0.91[CEU][hapmap]
rs2438978	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs2462774	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs2579519	0.91[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap]
rs2579549	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2579552	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692893	0.84[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692894	0.86[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2692934	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692935	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2692936	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917662	0.91[EUR][1000 genomes]
rs2918916	0.84[EUR][1000 genomes]
rs2969491	0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3111873	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3821051	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs4144055	0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs4426564	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[TSI][hapmap]
rs4527246	0.91[CEU][hapmap]
rs4907288	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap]
rs4907297	0.82[AFR][1000 genomes]
rs4907299	0.81[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs6740563	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap]
rs7561198	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7604842	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs893173	0.82[CHB][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874672	chr2:96637870-96809331	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv874674	chr2:96651163-96741944	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1825266	chr2:96704118-96830753	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv1004129	chr2:96738585-96825363	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
8	nsv1000049	chr2:96740430-96796312	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
10	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
11	nsv874675	chr2:96741944-96825363	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2579550	FER1L5	cis	cerebellum	SCAN
rs2579550	ZNF514	cis	parietal	SCAN
rs2579550	ZNF514	cis	cerebellum	SCAN
rs2579550	GPAT2	cis	Adipose Subcutaneous	GTEx
rs2579550	FAHD2CP	cis	lung	GTEx
rs2579550	GPAT2	cis	Muscle Skeletal	GTEx
rs2579550	ADRA2B	cis	Thyroid	GTEx
rs2579550	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs2579550	FAHD2CP	cis	Muscle Skeletal	GTEx
rs2579550	ADRA2B	cis	Nerve Tibial	GTEx
rs2579550	MGAT4A	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96734200-96749400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:96734400-96758000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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