Variant report

Variant	rs947242
Chromosome Location	chr1:58042849-58042850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12404408	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1341321	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1404388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1524705	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1524720	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.83[MKK][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1524729	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1524731	0.83[YRI][hapmap]
rs1534048	0.83[YRI][hapmap]
rs17115761	1.00[CEU][hapmap]
rs17116089	0.94[MEX][hapmap];0.81[AMR][1000 genomes]
rs1829986	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691445	0.81[LWK][hapmap];0.82[MKK][hapmap]
rs2691447	0.91[ASW][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap]
rs2691448	0.83[YRI][hapmap]
rs2691454	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2793624	0.88[LWK][hapmap];0.80[MKK][hapmap]
rs2793641	0.88[LWK][hapmap];0.80[MKK][hapmap]
rs2805850	0.81[MKK][hapmap]
rs2805860	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs3958553	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6681521	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7550226	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv523574	chr1:58018103-58087789	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv871684	chr1:58021206-58096379	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs947242	MDK	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58039200-58046800	Enhancers	Stomach Mucosa	stomach
2	chr1:58042000-58043000	Enhancers	Fetal Intestine Small	intestine
3	chr1:58042000-58044200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:58042000-58044800	Enhancers	Duodenum Mucosa	Duodenum
5	chr1:58042600-58043400	Enhancers	Small Intestine	intestine
6	chr1:58042600-58043600	Weak transcription	Fetal Intestine Large	intestine
7	chr1:58042800-58051600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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