Variant report

Variant	rs12702405
Chromosome Location	chr7:48045367-48045368
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:48044680..48047190-chr7:48067195..48070779,3	K562	blood:

Variant related genes	Relation type
ENSG00000164744	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10225968	0.83[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs10247913	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10253220	0.80[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs10253238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10256256	0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10261930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10951937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10951938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10951940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10951941	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10951942	0.89[JPT][hapmap];0.95[EUR][1000 genomes]
rs11761275	0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11762077	0.80[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11764799	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11766144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11766891	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11767002	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11768277	0.84[CEU][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11772387	0.83[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11772633	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11773348	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12535580	0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12537979	0.86[CEU][hapmap];0.94[JPT][hapmap]
rs12702406	0.80[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1318327	0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13230023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1574242	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915960	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915962	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1915965	0.88[JPT][hapmap]
rs1915966	0.84[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.99[EUR][1000 genomes]
rs1915967	0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1915968	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1915971	0.80[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1915972	0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2037482	0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2140113	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2348666	0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2348667	0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2348669	0.80[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2348670	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708909	0.80[EUR][1000 genomes]
rs2881991	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2881992	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4332046	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4618593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6978838	0.80[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6979699	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7357251	0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7357327	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7456745	0.80[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7779252	0.87[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7791084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7791572	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7791823	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7800590	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7807611	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7807612	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7807654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7807750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7808462	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9690905	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv888004	chr7:48028771-48120717	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12702405	C7orf57	cis	Esophagus Mucosa	GTEx
rs12702405	UPP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48031800-48050200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:48040000-48046600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:48043800-48046000	Enhancers	Stomach Mucosa	stomach
4	chr7:48043800-48046200	Enhancers	Fetal Intestine Small	intestine
5	chr7:48044000-48045800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr7:48044000-48046400	Enhancers	Duodenum Mucosa	Duodenum
7	chr7:48044000-48047000	Enhancers	GM12878-XiMat	blood
8	chr7:48044400-48046600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:48044800-48045400	Weak transcription	Small Intestine	intestine
10	chr7:48044800-48045800	Weak transcription	Fetal Lung	lung
11	chr7:48045000-48047000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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