Variant report

Variant	rs7530662
Chromosome Location	chr1:158167309-158167310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10489821	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs10489823	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs12040592	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs12409273	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12723141	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1570699	0.92[CEU][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs1633141	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1633149	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs16839951	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16840041	1.00[ASW][hapmap]
rs1748383	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1748387	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2269714	1.00[ASW][hapmap]
rs2518477	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs3021478	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3087210	0.92[CEU][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs3087211	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs3087212	0.92[CEU][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs3087213	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3118165	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs3136533	1.00[ASW][hapmap]
rs3138107	0.85[LWK][hapmap]
rs368130	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs374513	1.00[CEU][hapmap]
rs374686	0.82[CHB][hapmap]
rs377795	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs383688	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs384414	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs389495	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs393304	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs401904	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs402699	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs406558	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs407309	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs407980	0.82[CHB][hapmap]
rs413557	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs429201	0.82[CHB][hapmap]
rs434570	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs440862	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs448005	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs448556	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs449838	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs55819216	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56379344	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs594364	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs607948	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs614164	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs620699	0.82[CHB][hapmap]
rs623215	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs6671299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6680015	0.86[ASN][1000 genomes]
rs6703151	0.86[ASN][1000 genomes]
rs691077	0.90[CEU][hapmap]
rs691175	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs691314	0.82[CHB][hapmap]
rs691551	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs72711999	0.83[AMR][1000 genomes]
rs7513330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7527480	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7548147	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7550767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs859003	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs859005	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs859008	0.92[CEU][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs859009	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs859010	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs859013	0.92[CEU][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872480	chr1:158153526-158450238	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv13585	chr1:158159222-158214160	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1814455	chr1:158160528-158200312	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv508626	chr1:158161932-158242158	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158164000-158172800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:158166000-158168600	Weak transcription	Thymus	Thymus
3	chr1:158166000-158169800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:158166600-158167400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:158166600-158168000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:158167200-158167400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr1:158167200-158169200	Genic enhancers	Dnd41	blood
8	chr1:158167200-158169400	Strong transcription	Fetal Thymus	thymus
9	chr1:158167200-158170400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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