Variant report

Variant	rs7295717
Chromosome Location	chr12:120476434-120476435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120465481..120467971-chr12:120475425..120477605,2	K562	blood:
2	chr12:120475158..120477800-chr12:120503210..120505823,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10128766	0.83[CHB][hapmap]
rs10400498	0.83[CHB][hapmap]
rs10744747	0.93[ASN][1000 genomes]
rs10849732	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs10849735	0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs10849736	0.83[CHB][hapmap]
rs11064986	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11064998	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11065003	0.83[CHB][hapmap]
rs11065004	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065014	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11065017	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065018	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12310591	0.86[EUR][1000 genomes]
rs12311327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12320072	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12422923	0.85[EUR][1000 genomes]
rs2240311	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2393570	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2893812	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs3742044	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3759399	0.87[ASN][1000 genomes]
rs3852586	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3852588	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3886910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3999575	0.86[ASN][1000 genomes]
rs4105713	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4351876	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4767870	0.87[CHB][hapmap];0.94[ASN][1000 genomes]
rs4767873	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767875	0.83[EUR][1000 genomes]
rs6490278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6490280	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6490281	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6490283	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6490284	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7298183	0.85[EUR][1000 genomes]
rs7302874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7304325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs7305625	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7306739	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312811	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7312971	0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs7314959	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7956436	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958497	0.86[GIH][hapmap];0.82[ASN][1000 genomes]
rs7960725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961738	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7962812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7968557	0.82[CHB][hapmap]
rs7971249	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7977281	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978927	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active 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	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7295717	CIT	cis	frontal cortex	BrainEAC

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120454000-120478800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:120454200-120477800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:120454200-120478400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:120454200-120484800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:120454600-120479600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:120462400-120478600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:120463600-120479000	Weak transcription	Primary T cells from cord blood	blood
8	chr12:120472800-120478000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:120475800-120479200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:120476000-120477800	Weak transcription	HepG2	liver
11	chr12:120476200-120479200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:120476200-120479200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:120476200-120479200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:120476200-120479200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:120476200-120479200	Weak transcription	HMEC	breast

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