Variant report

Variant	rs398703
Chromosome Location	chr3:50574213-50574214
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	chr3:50571719..50574325-chr3:50657632..50660036,2	K562	blood:

Extended variants
information (count: 120 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1034405	0.94[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11719998	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12490042	0.83[CEU][hapmap]
rs12491425	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493985	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs129310	0.94[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13076850	0.86[EUR][1000 genomes]
rs13083004	0.84[EUR][1000 genomes]
rs13084476	0.89[EUR][1000 genomes]
rs13087550	0.83[CEU][hapmap]
rs13091933	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs13094336	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1385025	0.82[JPT][hapmap]
rs175634	0.83[ASW][hapmap];0.89[CEU][hapmap];0.90[CHD][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17787569	0.94[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs1824281	0.82[JPT][hapmap]
rs201193	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs201194	0.89[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs201196	0.86[EUR][1000 genomes]
rs201198	0.94[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2227280	0.85[EUR][1000 genomes]
rs2232248	0.94[CEU][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2232253	0.85[EUR][1000 genomes]
rs2236953	0.83[CEU][hapmap]
rs2236956	0.83[CEU][hapmap]
rs2236957	0.82[CEU][hapmap]
rs2236958	0.81[CEU][hapmap]
rs2236959	0.82[CEU][hapmap]
rs2236961	0.82[CEU][hapmap]
rs2236963	0.83[CEU][hapmap]
rs2236967	0.83[CEU][hapmap]
rs2236968	0.83[CEU][hapmap]
rs2236975	0.83[CEU][hapmap]
rs2236988	0.83[CEU][hapmap]
rs2269505	0.88[ASW][hapmap];0.94[CEU][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2269507	0.85[EUR][1000 genomes]
rs2282756	0.83[CEU][hapmap]
rs2282758	0.83[CEU][hapmap]
rs2355321	0.85[EUR][1000 genomes]
rs2355323	0.94[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34202063	0.85[EUR][1000 genomes]
rs34267788	0.85[EUR][1000 genomes]
rs34399912	0.85[EUR][1000 genomes]
rs34434811	0.85[EUR][1000 genomes]
rs34584636	0.94[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs34756253	0.89[EUR][1000 genomes]
rs34889917	0.85[EUR][1000 genomes]
rs35655236	0.84[EUR][1000 genomes]
rs35690191	0.84[EUR][1000 genomes]
rs35714264	0.90[EUR][1000 genomes]
rs35864641	0.85[EUR][1000 genomes]
rs375544	0.88[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs3792328	0.88[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs3804627	0.94[ASW][hapmap];0.94[CEU][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs391620	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3943212	0.82[JPT][hapmap]
rs396302	0.88[ASW][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs399484	0.94[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs399971	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs414171	0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs417592	0.94[CEU][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs441516	0.94[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs443030	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs443436	0.81[JPT][hapmap]
rs448028	0.82[JPT][hapmap]
rs4533647	0.85[EUR][1000 genomes]
rs453570	0.94[ASW][hapmap];0.94[CEU][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4688712	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688719	0.82[CEU][hapmap]
rs490634	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs59949730	0.85[EUR][1000 genomes]
rs628081	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6446212	0.88[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs6446213	0.83[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs67425923	0.80[EUR][1000 genomes]
rs67588094	0.85[EUR][1000 genomes]
rs6778680	0.81[JPT][hapmap]
rs6779819	0.83[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs67813889	0.87[EUR][1000 genomes]
rs6784166	0.90[EUR][1000 genomes]
rs6787521	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs6787890	0.83[CEU][hapmap]
rs6791880	0.86[TSI][hapmap]
rs6796769	0.83[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs695170	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71326937	0.85[EUR][1000 genomes]
rs728901	0.82[JPT][hapmap]
rs73082948	0.83[EUR][1000 genomes]
rs750453	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs750510	0.94[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754298	0.82[ASW][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7615703	0.83[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs762895	0.83[CEU][hapmap]
rs762897	0.82[CEU][hapmap]
rs762898	0.83[CEU][hapmap]
rs7646236	0.94[ASW][hapmap];0.94[CEU][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs809454	0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs813243	0.88[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs900735	0.82[JPT][hapmap]
rs916217	0.83[CEU][hapmap]
rs929047	0.83[CEU][hapmap]
rs9682401	0.82[JPT][hapmap]
rs9825535	0.83[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap]
rs9826757	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
6	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
15	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs398703	CAMP	cis	cerebellum	SCAN
rs398703	HEMK1	cis	parietal	SCAN
rs398703	ALS2CL	cis	parietal	SCAN
rs398703	APEH	cis	cerebellum	SCAN
rs398703	HEMK1	cis	cerebellum	SCAN
rs398703	MST1	cis	cerebellum	SCAN
rs398703	NBEAL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50567600-50574400	Weak transcription	Spleen	Spleen
2	chr3:50570200-50575000	Weak transcription	Fetal Kidney	kidney
3	chr3:50570200-50576400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:50571400-50576400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:50571600-50576200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:50571800-50576000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:50571800-50576400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:50572400-50575400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:50572600-50576000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:50573600-50574800	Enhancers	K562	blood
11	chr3:50573800-50574600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:50574200-50574400	Enhancers	Esophagus	oesophagus
13	chr3:50574200-50574400	Bivalent Enhancer	Fetal Stomach	stomach
14	chr3:50574200-50574400	Bivalent Enhancer	HSMMtube	muscle
15	chr3:50574200-50574600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:50574200-50574800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:50574200-50575000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:50574200-50575000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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