Variant report

Variant	rs2297487
Chromosome Location	chr1:152734390-152734391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152728900..152731516-chr1:152732979..152735193,2	MCF-7	breast:
2	chr1:152626242..152627151-chr1:152734184..152735164,3	MCF-7	breast:
3	chr1:152733924..152735488-chr1:152736776..152739020,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203786	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1048534	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888515	0.83[ASN][1000 genomes]
rs11205099	0.86[CHD][hapmap]
rs11205105	0.83[CEU][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap]
rs11205108	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11205109	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12023710	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12036241	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12045361	0.82[ASN][1000 genomes]
rs12046205	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12046231	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12046930	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12094590	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12568028	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1332505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1332506	0.84[CHD][hapmap]
rs1412543	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1412545	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16834421	0.90[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16834461	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.98[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]
rs16834495	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1888293	0.82[ASN][1000 genomes]
rs1888962	0.83[ASN][1000 genomes]
rs1953057	0.84[CHD][hapmap]
rs2010006	0.83[ASN][1000 genomes]
rs41268474	0.81[EUR][1000 genomes]
rs4845323	0.82[ASN][1000 genomes]
rs4845475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845479	0.86[CHD][hapmap]
rs4845481	0.86[CHD][hapmap]
rs4845484	0.82[EUR][1000 genomes]
rs4845487	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6587703	0.86[ASN][1000 genomes]
rs6689049	0.86[CHD][hapmap]
rs6698773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7411365	0.80[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs7515777	0.84[CHD][hapmap]
rs7549803	1.00[CEU][hapmap];0.80[CHD][hapmap];0.93[MEX][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs872180	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs913997	0.83[ASN][1000 genomes]
rs913998	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs913999	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs944683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs950337	0.90[CEU][hapmap];0.80[CHD][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv33483	chr1:152550269-152775526	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv547891	chr1:152556085-152770446	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv428521	chr1:152663153-152831578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv947325	chr1:152670204-152793272	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv34854	chr1:152671913-152756806	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv818478	chr1:152672005-152734796	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	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
14	esv2756865	chr1:152682708-152739226	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	esv2763813	chr1:152687058-152780522	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1000648	chr1:152719318-152747126	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv508615	chr1:152724155-152787503	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
18	nsv1004884	chr1:152724514-152780522	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2297487	SPRR1A	cis	parietal	SCAN
rs2297487	LYSMD1	cis	parietal	SCAN
rs2297487	LCE1E	cis	lymphoblastoid	seeQTL
rs2297487	TPM3	cis	cerebellum	SCAN
rs2297487	CRTC2	cis	parietal	SCAN
rs2297487	LCE1F	cis	cerebellum	SCAN
rs2297487	JTB	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152729000-152735000	Enhancers	HMEC	breast
2	chr1:152729200-152735000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:152730600-152734600	Enhancers	Esophagus	oesophagus
4	chr1:152732000-152734800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:152732800-152734800	Enhancers	NHEK	skin
6	chr1:152733000-152734400	Enhancers	Placenta	Placenta
7	chr1:152734000-152734800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:152734200-152734400	Enhancers	HSMM	muscle
9	chr1:152734200-152735000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:152734200-152735000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:152734200-152735000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:152734200-152735000	Enhancers	NHLF	lung

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