Variant report

Variant	rs28924721
Chromosome Location	chr1:152974254-152974255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr1:152973846-152974262	K562	blood:	n/a	chr1:152974054-152974062 chr1:152974127-152974141 chr1:152974069-152974078 chr1:152974050-152974061 chr1:152974052-152974064
2	GATA3	chr1:152973753-152974269	MCF-7	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRR1A-2	chr1:152974225-152974269	NONHSAT006502

Variant related genes	Relation type
SPRR3	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10788850	0.83[TSI][hapmap]
rs10888528	0.88[CHB][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs10888529	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs1108410	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11205179	0.84[EUR][1000 genomes]
rs11205180	0.83[EUR][1000 genomes]
rs11205181	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11205182	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs1129655	0.81[TSI][hapmap]
rs11488175	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs11576797	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap]
rs11581802	0.80[ASN][1000 genomes]
rs11587269	0.92[CEU][hapmap]
rs11590835	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11812015	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs12079087	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12082627	0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12083211	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs12734348	0.88[CHB][hapmap]
rs1413849	0.83[TSI][hapmap]
rs1415959	0.83[TSI][hapmap]
rs1415960	0.83[TSI][hapmap]
rs1415961	0.83[TSI][hapmap]
rs1415972	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[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500937	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1577960	0.83[EUR][1000 genomes]
rs1611753	0.83[TSI][hapmap]
rs1611759	0.81[TSI][hapmap]
rs1611760	0.83[TSI][hapmap]
rs1611764	0.83[TSI][hapmap]
rs1995308	0.88[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2050673	0.84[CEU][hapmap]
rs2339491	0.83[TSI][hapmap]
rs3737864	0.81[AMR][1000 genomes]
rs3737867	0.83[TSI][hapmap]
rs3753454	0.83[TSI][hapmap]
rs3806219	0.83[TSI][hapmap]
rs4041402	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41263664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240867	0.83[TSI][hapmap]
rs4845503	0.95[EUR][1000 genomes]
rs4845505	0.95[EUR][1000 genomes]
rs4845513	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs56158137	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56412380	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61811886	0.81[AMR][1000 genomes]
rs61813181	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61813182	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587724	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6660878	0.83[EUR][1000 genomes]
rs6661059	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6664380	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs6670614	0.83[TSI][hapmap]
rs6671414	0.83[TSI][hapmap]
rs6671520	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673356	0.84[CEU][hapmap];0.88[CHB][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs6675009	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs6683514	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6684188	0.83[TSI][hapmap]
rs6686526	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs6692062	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs6693927	0.84[CEU][hapmap];0.88[CHB][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs6698361	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6704105	0.83[TSI][hapmap]
rs7531076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7532166	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7540609	0.83[EUR][1000 genomes]
rs7543689	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs7548977	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7551791	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs946098	0.83[TSI][hapmap]
rs946099	0.83[TSI][hapmap]
rs946100	0.83[TSI][hapmap]
rs946101	0.83[TSI][hapmap]
rs9659623	0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
10	nsv1003756	chr1:152944201-153044621	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv3416199	chr1:152957887-153005113	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28924721	S100A6	cis	cerebellum	SCAN
rs28924721	PGLYRP4	cis	parietal	SCAN
rs28924721	RAB13	cis	parietal	SCAN
rs28924721	ATP8B2	cis	parietal	SCAN
rs28924721	BNIPL	cis	cerebellum	SCAN
rs28924721	S100A7	cis	cerebellum	SCAN
rs28924721	C1orf43	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152970600-152974800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:152970600-152975600	Enhancers	Placenta Amnion	Placenta Amnion
3	chr1:152973600-152974400	Enhancers	Placenta	Placenta
4	chr1:152973600-152974600	Weak transcription	Esophagus	oesophagus

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