Variant report

Variant	rs7538295
Chromosome Location	chr1:153224233-153224234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10159119	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10494291	0.80[EUR][1000 genomes]
rs10494292	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs10494293	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs10494294	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs10494295	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10494296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10494297	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10788862	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs10888536	0.80[EUR][1000 genomes]
rs10888537	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs10888538	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs10888539	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs11205219	0.80[EUR][1000 genomes]
rs11205222	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs11205223	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs11205225	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs11205227	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs11205228	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11205229	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs11205230	0.80[EUR][1000 genomes]
rs11205231	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs11205232	0.83[EUR][1000 genomes]
rs11205238	0.84[EUR][1000 genomes]
rs11205248	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11205251	0.87[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs11205252	0.86[YRI][hapmap]
rs1143390	0.84[LWK][hapmap];0.89[YRI][hapmap]
rs11583156	0.83[EUR][1000 genomes]
rs11583609	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11589914	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12043009	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12058098	0.80[EUR][1000 genomes]
rs12062833	0.80[EUR][1000 genomes]
rs12069007	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs12122588	0.84[EUR][1000 genomes]
rs12127862	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs12134915	0.84[EUR][1000 genomes]
rs12136409	0.84[EUR][1000 genomes]
rs12142970	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12740666	0.80[EUR][1000 genomes]
rs12747804	0.84[EUR][1000 genomes]
rs12755266	0.80[EUR][1000 genomes]
rs12760683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1329094	0.80[EUR][1000 genomes]
rs1329099	0.84[EUR][1000 genomes]
rs1329100	0.84[EUR][1000 genomes]
rs1410859	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs16835073	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs16835081	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs16835083	0.84[EUR][1000 genomes]
rs16835093	0.83[CEU][hapmap];0.90[MEX][hapmap];0.84[EUR][1000 genomes]
rs2094638	0.86[YRI][hapmap]
rs34119886	0.84[EUR][1000 genomes]
rs35287517	0.80[EUR][1000 genomes]
rs35358388	0.84[EUR][1000 genomes]
rs71626758	0.84[EUR][1000 genomes]
rs873234	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription 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	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1004168	chr1:153088209-153226033	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1003014	chr1:153209833-153263691	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv535172	chr1:153209833-153263691	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv998032	chr1:153210770-153264131	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3323848	chr1:153221028-153225326	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
13	esv3450708	chr1:153221928-153224626	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7538295	HIST2H2AC	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153223400-153225800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:153223600-153225000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr1:153224000-153224400	Enhancers	Esophagus	oesophagus
4	chr1:153224000-153224800	Enhancers	GM12878-XiMat	blood
5	chr1:153224200-153227800	Weak transcription	Fetal Brain Male	brain

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