Variant report

Variant	rs7980769
Chromosome Location	chr12:25338943-25338944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10505959	0.91[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap]
rs10743548	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10771166	1.00[CHB][hapmap]
rs10771174	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10771175	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs10771176	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs10771183	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842464	1.00[CHB][hapmap]
rs10842468	0.88[JPT][hapmap]
rs10842470	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10842490	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10842494	1.00[YRI][hapmap]
rs10842495	0.82[AMR][1000 genomes]
rs10842496	0.83[ASW][hapmap];0.83[MKK][hapmap]
rs10842503	0.85[ASN][1000 genomes]
rs10842515	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10842516	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10842517	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11047825	0.88[CHB][hapmap]
rs11047858	0.89[CHB][hapmap]
rs11047878	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047879	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047903	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047904	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047908	0.87[ASN][1000 genomes]
rs11047912	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11047914	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11047917	1.00[JPT][hapmap]
rs1137282	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11834088	1.00[CHB][hapmap]
rs11836509	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12227966	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12228638	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]
rs12367971	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs1497253	0.89[CHB][hapmap]
rs17388573	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17388587	1.00[JPT][hapmap]
rs17389103	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2220196	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs3924650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4313666	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs4368021	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4606562	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55950027	0.81[AMR][1000 genomes]
rs61761150	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7133640	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7134616	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap]
rs7298444	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7299998	0.87[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs7303373	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs7303669	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs7306769	0.92[MKK][hapmap];1.00[YRI][hapmap]
rs7309670	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7315339	0.92[ASW][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7960428	1.00[CHB][hapmap]
rs7960917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7964623	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7965763	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968023	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7971062	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7971288	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7973450	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973623	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7975271	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs7976254	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs7976355	1.00[JPT][hapmap]
rs7977616	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7980834	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv515612	chr12:25272027-25341177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv557797	chr12:25272027-25341177	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7980769	SSPN	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25338600-25339400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:25338800-25339400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:25338800-25339400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr12:25338800-25339600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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