Variant report

Variant	rs16834421
Chromosome Location	chr1:152712747-152712748
allele	A/G
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	FOS	chr1:152712288-152712751	MCF10A-Er-Src	breast:	n/a	chr1:152712521-152712530 chr1:152712520-152712532
2	CTCF	chr1:152712640-152712790	HMF	breast:	n/a	n/a
3	EBF1	chr1:152712392-152712784	GM12878	blood:	n/a	chr1:152712537-152712546 chr1:152712536-152712546 chr1:152712616-152712626 chr1:152712535-152712546 chr1:152712614-152712627 chr1:152712616-152712625 chr1:152712537-152712546 chr1:152712535-152712548
4	CTCF	chr1:152712660-152712810	HA-sp	spinal cord:	n/a	n/a
5	MYC	chr1:152712312-152712781	MCF10A-Er-Src	breast:	n/a	chr1:152712522-152712531

No.	Distal block	Cell Line	Cell type
1	chr1:152711224..152713888-chr1:152737781..152739633,2	MCF-7	breast:
2	chr1:152703574..152706354-chr1:152711144..152714004,3	MCF-7	breast:
3	chr1:152700584..152702485-chr1:152711586..152714086,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233819	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1048534	0.90[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10888515	0.80[ASN][1000 genomes]
rs11205105	0.83[CHD][hapmap]
rs11205108	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11205109	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12023710	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12034091	0.82[MEX][hapmap]
rs12036241	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12046205	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12046231	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12046930	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12094590	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12568028	0.90[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1332505	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1412545	0.90[CEU][hapmap]
rs16834461	0.90[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16834495	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297487	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]
rs4845323	0.80[CHD][hapmap]
rs4845475	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845487	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6698773	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7411365	0.81[TSI][hapmap]
rs7549803	0.90[CEU][hapmap];0.83[CHD][hapmap]
rs872180	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs913998	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs913999	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs944683	0.90[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs950337	0.83[CHD][hapmap]

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	nsv469873	chr1:152563260-152713616	ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv482518	chr1:152563260-152713616	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	esv3692902	chr1:152669367-152732567	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	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
18	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs16834421	CRTC2	cis	parietal	SCAN
rs16834421	SMCP	cis	cerebellum	SCAN
rs16834421	LYSMD1	cis	parietal	SCAN
rs16834421	LCE1F	cis	cerebellum	SCAN
rs16834421	TPM3	cis	cerebellum	SCAN
rs16834421	JTB	cis	cerebellum	SCAN
rs16834421	LCE1E	cis	lymphoblastoid	seeQTL
rs16834421	LCE1E	cis	multi-tissue	Pritchard
rs16834421	SPRR1A	cis	parietal	SCAN
rs16834421	RPTN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152710200-152714400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:152711600-152713200	Enhancers	NHLF	lung
3	chr1:152711600-152718600	Enhancers	HMEC	breast
4	chr1:152711800-152712800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:152711800-152713000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:152711800-152713000	Enhancers	NHEK	skin
7	chr1:152712000-152713000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:152712400-152713000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:152712600-152715800	Weak transcription	NHDF-Ad	bronchial

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