Variant report

Variant	rs11724758
Chromosome Location	chr4:120239878-120239879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120234842..120237819-chr4:120239424..120241485,2	K562	blood:

Extended variants
information (count: 146 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10003567	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10005237	0.85[ASN][1000 genomes]
rs10006259	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10006525	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs10006706	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs10006877	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs10013042	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10015883	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10017335	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs10024933	0.80[ASN][1000 genomes]
rs10030660	0.86[CHB][hapmap]
rs10031483	0.86[CHB][hapmap]
rs10032299	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1011054	0.91[CHD][hapmap]
rs10212775	0.85[ASN][1000 genomes]
rs10213158	0.80[ASN][1000 genomes]
rs10213267	0.85[ASN][1000 genomes]
rs1022145	0.84[ASN][1000 genomes]
rs10518300	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10518328	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs1052633	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11098497	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11098498	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11098499	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs11098501	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11098502	0.80[ASN][1000 genomes]
rs11722872	0.84[ASN][1000 genomes]
rs11724409	0.80[ASN][1000 genomes]
rs11729521	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs11731571	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11732087	0.85[ASN][1000 genomes]
rs11732621	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11732686	0.88[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs11734241	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs11737400	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11935596	0.86[CHB][hapmap]
rs11944880	0.91[CHD][hapmap]
rs12498994	0.80[ASN][1000 genomes]
rs12502423	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs12506610	0.85[ASN][1000 genomes]
rs12507565	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12507964	0.86[CHB][hapmap]
rs12508504	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs12509621	0.80[ASN][1000 genomes]
rs12510138	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs12510269	0.85[ASN][1000 genomes]
rs12511640	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12513083	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs12711071	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs13104219	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs13113112	0.91[CHD][hapmap]
rs13113885	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13117947	0.80[AFR][1000 genomes]
rs13134517	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs13134665	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs13149954	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1383532	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs1480931	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs1480933	0.84[TSI][hapmap]
rs1511017	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1511018	0.91[CHD][hapmap]
rs1511019	0.91[CHD][hapmap]
rs1511025	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1546502	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs1546503	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1546504	0.82[ASN][1000 genomes]
rs1546505	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs1546506	0.84[ASN][1000 genomes]
rs17006190	0.86[CHB][hapmap]
rs17049949	0.80[ASN][1000 genomes]
rs17595608	0.80[ASN][1000 genomes]
rs1814815	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1980024	0.80[ASN][1000 genomes]
rs1980025	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1980026	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1980027	0.80[ASN][1000 genomes]
rs2017058	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2036856	0.80[ASN][1000 genomes]
rs2036857	0.80[ASN][1000 genomes]
rs2036858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2036860	0.80[ASN][1000 genomes]
rs2175383	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291185	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs2389803	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs2389809	0.86[CHB][hapmap]
rs28363929	0.80[ASN][1000 genomes]
rs28373117	0.80[ASN][1000 genomes]
rs28439855	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28580295	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28643450	0.80[ASN][1000 genomes]
rs28652763	0.85[ASN][1000 genomes]
rs28713555	0.80[ASN][1000 genomes]
rs2892848	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs2964	0.85[ASN][1000 genomes]
rs3733519	0.89[CHB][hapmap]
rs3733524	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs3749591	0.89[CHD][hapmap]
rs3775843	0.81[CHB][hapmap]
rs3775844	0.86[CHB][hapmap]
rs3775845	0.86[CHB][hapmap]
rs4107728	0.80[ASN][1000 genomes]
rs4443261	0.80[ASN][1000 genomes]
rs4472123	0.85[ASN][1000 genomes]
rs4643791	0.82[AFR][1000 genomes]
rs4833613	0.84[CEU][hapmap]
rs62320740	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66900435	0.80[ASN][1000 genomes]
rs6822808	0.94[CHB][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6834796	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs6837898	0.91[CHD][hapmap]
rs6843229	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[TSI][hapmap]
rs6843509	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6847248	0.82[ASN][1000 genomes]
rs6848389	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs6849171	0.86[CHB][hapmap]
rs6849561	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs6849889	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs6857105	0.81[ASN][1000 genomes]
rs714899	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7659403	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7659501	0.86[CHB][hapmap]
rs7672129	0.81[ASN][1000 genomes]
rs7672594	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7672778	0.80[ASN][1000 genomes]
rs7673476	0.80[ASN][1000 genomes]
rs7681544	0.86[CHB][hapmap]
rs7687843	0.86[CHB][hapmap]
rs7689729	0.80[ASN][1000 genomes]
rs7699064	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs878372	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs878373	0.83[ASN][1000 genomes]
rs878376	0.85[ASN][1000 genomes]
rs907204	0.85[ASN][1000 genomes]
rs907205	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs938056	0.83[ASN][1000 genomes]
rs9991166	0.85[ASN][1000 genomes]
rs9991959	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs9996494	0.83[ASN][1000 genomes]
rs9996644	0.83[ASN][1000 genomes]
rs9998585	0.86[CHB][hapmap]
rs9999724	0.81[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879840	chr4:120227419-120257417	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11724758	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs11724758	BBS7	cis	parietal	SCAN
rs11724758	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs11724758	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs11724758	TRPC3	cis	parietal	SCAN
rs11724758	USP53	cis	parietal	SCAN
rs11724758	SYNPO2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120222000-120251000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:120222200-120244600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:120222400-120240800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:120222800-120240800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:120235600-120251000	Weak transcription	Left Ventricle	heart
6	chr4:120235800-120241800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:120238800-120240000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:120239000-120243800	Active TSS	Fetal Intestine Small	intestine
9	chr4:120239600-120240000	Flanking Active TSS	Fetal Intestine Large	intestine
10	chr4:120239800-120244000	Active TSS	Duodenum Mucosa	Duodenum

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