Variant report

Variant	rs3749500
Chromosome Location	chr7:56607497-56607498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10215049	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215705	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10226486	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10226756	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10232356	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10235121	0.88[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs10236798	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10242086	0.88[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs10249023	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10256440	0.88[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10259576	0.82[ASW][hapmap];0.90[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs10266889	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10269082	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10272852	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10281482	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10282398	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105304	0.93[EUR][1000 genomes]
rs1105305	0.89[ASW][hapmap];0.90[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs1105306	0.93[EUR][1000 genomes]
rs11976165	0.90[CHB][hapmap]
rs11977998	0.91[EUR][1000 genomes]
rs11978242	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12155162	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12155169	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12719002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12719003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227258	0.96[YRI][hapmap]
rs13229926	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13231784	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13245583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13307736	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13312340	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1352444	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387067	0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1532083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1601913	0.90[CHB][hapmap]
rs1606628	0.90[CHB][hapmap]
rs1849671	0.81[CHB][hapmap]
rs1849672	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs1906626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906629	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34135483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34270096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34340801	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34593554	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34765785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35043412	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35483986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749502	0.93[ASN][1000 genomes]
rs3828495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285439	0.93[EUR][1000 genomes]
rs4442091	0.93[EUR][1000 genomes]
rs4947553	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56869388	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66831640	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67173162	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6944931	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6952677	0.93[EUR][1000 genomes]
rs6952857	0.93[EUR][1000 genomes]
rs6955935	0.90[EUR][1000 genomes]
rs6957076	0.90[EUR][1000 genomes]
rs6957105	0.93[EUR][1000 genomes]
rs6968161	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6968398	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7357108	0.95[CEU][hapmap];0.89[YRI][hapmap]
rs7458882	0.91[EUR][1000 genomes]
rs7782035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782889	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7783143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796117	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7799034	0.90[CHB][hapmap]
rs7804839	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656713	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656714	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526294	chr7:56171489-56622630	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1016771	chr7:56174828-56643856	Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv538862	chr7:56174828-56643856	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1033163	chr7:56307057-56677865	ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv538863	chr7:56307057-56677865	ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427783	chr7:56334626-56983646	Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv1022563	chr7:56383876-57318888	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
8	nsv1016255	chr7:56453095-56835595	ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv888066	chr7:56466740-56693762	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1028678	chr7:56511649-56795206	ZNF genes & repeats Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv538864	chr7:56511649-56795206	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv1020833	chr7:56511848-57323499	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
13	nsv538865	chr7:56511848-57323499	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
14	nsv8090	chr7:56511877-56772523	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv1017561	chr7:56512618-57334136	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
16	esv3432	chr7:56561673-56611316	ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv831009	chr7:56566629-56754313	ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3749500	LANCL2	cis	cerebellum	SCAN
rs3749500	SEPT14	cis	cerebellum	SCAN
rs3749500	CHCHD2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56604800-56609600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:56605000-56611400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:56605200-56612600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
4	chr7:56605600-56608000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:56605600-56610600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:56606200-56609200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr7:56607200-56610600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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