Variant report

Variant	rs2348666
Chromosome Location	chr7:48078793-48078794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:48072450..48075424-chr7:48078443..48080669,2	K562	blood:

Variant related genes	Relation type
ENSG00000164746	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10225968	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs10247913	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253238	0.84[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10256256	0.84[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];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10261930	0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs10951937	0.81[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs10951938	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs10951940	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10951941	0.92[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10951942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11761275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11762077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11764799	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11766144	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11766891	0.94[EUR][1000 genomes]
rs11767002	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11768277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11772387	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11772633	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11773348	0.83[EUR][1000 genomes]
rs12535580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12537979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12702405	0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12702406	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1318327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13230023	0.84[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs1574242	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1915960	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs1915962	0.92[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1915965	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs1915966	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1915967	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915968	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2140113	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs2348667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2348669	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2348670	0.84[EUR][1000 genomes]
rs2708851	0.85[TSI][hapmap]
rs2708883	0.82[TSI][hapmap]
rs2708909	0.85[TSI][hapmap]
rs2881991	0.88[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2881992	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4332046	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4354227	0.81[AMR][1000 genomes]
rs4618593	0.89[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs6978838	1.00[CEU][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6979699	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7357251	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7357327	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7456745	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7779252	0.89[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7791084	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7791572	0.88[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7791823	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7807611	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7807612	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7807654	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7807750	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7808462	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9690905	0.92[CEU][hapmap];0.90[JPT][hapmap];0.94[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2348666	C7orf57	cis	Esophagus Mucosa	GTEx
rs2348666	PKD1L1	cis	parietal	SCAN
rs2348666	ABCA13	cis	parietal	SCAN
rs2348666	UPP1	cis	cerebellum	SCAN
rs2348666	UPP1	cis	Muscle Skeletal	GTEx
rs2348666	PKD1L1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48076200-48079600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:48076200-48079600	Weak transcription	HMEC	breast
3	chr7:48076200-48079600	Weak transcription	NHEK	skin
4	chr7:48076200-48080600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:48076200-48080800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:48078000-48080000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:48078000-48081000	Enhancers	H9 Cell Line	embryonic stem cell
8	chr7:48078200-48078800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:48078200-48079000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:48078200-48079200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr7:48078400-48078800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
12	chr7:48078400-48078800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr7:48078400-48078800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr7:48078400-48079000	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr7:48078400-48080000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr7:48078600-48079000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr7:48078600-48079800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:48078600-48083200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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