Variant report

Variant	rs1915960
Chromosome Location	chr7:48044478-48044479
allele	C/T
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	SMC3	chr7:48044378-48044547	GM12878	blood:	n/a	n/a
2	MYC	chr7:48044214-48044751	NB4	blood:	n/a	n/a
3	EP300	chr7:48044316-48044556	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SUN3	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10225968	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs10247913	0.95[EUR][1000 genomes]
rs10253220	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10253238	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10256256	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs10261930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10951937	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10951938	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10951940	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10951941	0.96[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]
rs10951942	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11761275	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs11762077	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs11764799	0.94[EUR][1000 genomes]
rs11766144	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11766891	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768277	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes]
rs11772387	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11772633	0.84[EUR][1000 genomes]
rs11773348	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12535580	0.96[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12537979	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs12702405	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]
rs12702406	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1318327	0.96[CEU][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes]
rs13230023	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1574242	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915962	0.96[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]
rs1915965	0.89[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap]
rs1915966	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1915967	0.96[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes]
rs1915968	0.99[EUR][1000 genomes]
rs1915971	0.96[CEU][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs1915972	0.96[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2037482	0.96[CEU][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes]
rs2140113	0.89[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap]
rs2348666	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs2348667	0.95[CEU][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes]
rs2348669	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2348670	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708883	0.83[TSI][hapmap]
rs2708909	0.81[TSI][hapmap]
rs2881991	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881992	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4332046	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618593	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6978838	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs6979699	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7357251	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7357327	0.99[EUR][1000 genomes]
rs7456745	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7779252	0.96[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7791084	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7791572	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7791823	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7800590	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7807611	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7807612	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7807654	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7807750	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7808462	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9690905	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1915960	ABCA13	cis	parietal	SCAN
rs1915960	UPP1	cis	cerebellum	SCAN
rs1915960	UPP1	cis	multi-tissue	Pritchard
rs1915960	PKD1L1	cis	cerebellum	SCAN
rs1915960	UPP1	cis	Muscle Skeletal	GTEx
rs1915960	PKD1L1	cis	parietal	SCAN

Chromatin state (count:23 , 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	chr7:48043200-48044800	Enhancers	Fetal Lung	lung
4	chr7:48043800-48044600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:48043800-48046000	Enhancers	Stomach Mucosa	stomach
6	chr7:48043800-48046200	Enhancers	Fetal Intestine Small	intestine
7	chr7:48044000-48044600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:48044000-48044600	Enhancers	Primary B cells from cord blood	blood
9	chr7:48044000-48044600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:48044000-48044600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:48044000-48044600	Enhancers	Fetal Stomach	stomach
12	chr7:48044000-48044800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr7:48044000-48045800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr7:48044000-48046400	Enhancers	Duodenum Mucosa	Duodenum
15	chr7:48044000-48047000	Enhancers	GM12878-XiMat	blood
16	chr7:48044200-48044600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:48044200-48044600	Enhancers	Gastric	stomach
18	chr7:48044200-48045000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr7:48044200-48045000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr7:48044200-48045200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr7:48044400-48044600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:48044400-48044800	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr7:48044400-48046600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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