Variant report

Variant	rs6690549
Chromosome Location	chr1:152930426-152930427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1015995	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1055935	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10788849	0.95[EUR][1000 genomes]
rs10788850	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10788853	0.90[CHB][hapmap]
rs10788855	0.82[CHB][hapmap]
rs10888524	0.82[CHB][hapmap]
rs10888525	0.82[CHB][hapmap]
rs10888526	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10888527	0.90[CHB][hapmap];0.86[GIH][hapmap]
rs11205143	0.85[EUR][1000 genomes]
rs11205174	0.90[CHB][hapmap]
rs11205175	0.90[CHB][hapmap]
rs11205177	0.89[CHB][hapmap]
rs1129655	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1134220	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs11576457	0.95[EUR][1000 genomes]
rs11803197	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12041126	0.93[ASN][1000 genomes]
rs12734348	0.89[CEU][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs12748969	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1334848	0.82[CHB][hapmap]
rs1334849	0.82[CHB][hapmap]
rs1334850	0.81[CHB][hapmap]
rs1413848	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1413849	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1415957	0.84[EUR][1000 genomes]
rs1415959	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1415960	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1415961	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1415965	0.90[CHB][hapmap]
rs1415966	0.90[CHB][hapmap]
rs1415968	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1611753	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1611759	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1611760	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1611762	0.82[CHB][hapmap]
rs1611764	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs1750309	0.90[CHB][hapmap]
rs1890285	0.90[CHB][hapmap]
rs1933382	0.90[CHB][hapmap]
rs1933383	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1984197	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1995308	0.82[CHB][hapmap]
rs1999886	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2050674	0.94[EUR][1000 genomes]
rs2066004	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs2066005	1.00[CEU][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2070964	0.80[CHB][hapmap]
rs2152993	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2225919	0.82[CHB][hapmap]
rs2339491	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2339493	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2339495	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2879489	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2879490	0.84[EUR][1000 genomes]
rs310103	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs310105	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs310109	0.86[CHB][hapmap]
rs310126	0.90[CHB][hapmap]
rs3170863	0.89[CEU][hapmap];0.90[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3181787	0.82[CHB][hapmap]
rs368912	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs3737867	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs3753454	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs377768	0.90[CHB][hapmap]
rs3806219	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs3806222	0.90[CHB][hapmap]
rs387930	0.90[CHB][hapmap]
rs394859	0.94[CHB][hapmap]
rs399550	0.90[CHB][hapmap]
rs409986	0.90[CHB][hapmap]
rs4240865	0.90[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap]
rs4240866	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs4240867	0.82[CHB][hapmap]
rs427470	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs431242	0.90[CHB][hapmap]
rs4363385	0.90[CHB][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs440598	0.90[CHB][hapmap]
rs441229	0.90[CHB][hapmap]
rs454245	0.90[CHB][hapmap]
rs472076	0.81[CHB][hapmap]
rs4845336	0.81[CHB][hapmap]
rs4845497	0.96[EUR][1000 genomes]
rs4845501	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845513	0.82[CHB][hapmap]
rs4845514	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4845515	0.81[CHB][hapmap]
rs4845519	0.82[CHB][hapmap]
rs56347903	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576941	0.90[CHB][hapmap]
rs58124215	0.94[EUR][1000 genomes]
rs581447	0.90[CHB][hapmap]
rs582345	0.90[CHB][hapmap]
rs608509	0.90[CHB][hapmap]
rs6587714	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662506	0.90[CHB][hapmap]
rs6656812	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664411	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6664823	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6667418	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6668311	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6670614	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6671414	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6671524	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6675352	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6684188	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6690672	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704105	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7546648	0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs7556517	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];0.98[ASN][1000 genomes]
rs756303	0.95[EUR][1000 genomes]
rs821755	0.90[CHB][hapmap]
rs883810	0.81[CEU][hapmap];0.87[GIH][hapmap];0.81[EUR][1000 genomes]
rs946098	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs946099	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs946100	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs946101	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs9659389	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs9659623	0.90[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv998873	chr1:152869127-152975258	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6690549	SMCP	cis	cerebellum	SCAN
rs6690549	BNIPL	cis	cerebellum	SCAN
rs6690549	LCE2B	cis	parietal	SCAN
rs6690549	PGLYRP4	cis	parietal	SCAN
rs6690549	C1orf54	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152927600-152931400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr1:152927600-152932600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:152927600-152932600	Weak transcription	HMEC	breast
4	chr1:152927800-152932400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:152927800-152932600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:152927800-152937000	Weak transcription	NHEK	skin

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