Variant report

Variant	rs6787890
Chromosome Location	chr3:50520128-50520129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1107265	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs11130250	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490042	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12492113	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494849	0.83[CEU][hapmap]
rs13087550	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13091933	0.83[CEU][hapmap]
rs13099869	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1467913	0.83[CEU][hapmap]
rs1467914	0.83[CEU][hapmap]
rs2027854	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236950	0.86[MEX][hapmap]
rs2236953	1.00[CEU][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2236954	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs2236955	0.94[CEU][hapmap]
rs2236956	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2236957	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs2236958	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2236959	0.94[CEU][hapmap]
rs2236961	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236962	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236963	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236964	0.94[CEU][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs2236965	0.94[CEU][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs2236967	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236968	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236971	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236973	0.94[CEU][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs2236975	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236979	0.94[CEU][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs2236981	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2236983	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2236984	0.94[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2236987	0.94[CEU][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2236988	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2282752	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs2282753	0.94[CEU][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs2282754	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs2282756	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes]
rs2282758	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2282760	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2282762	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2298955	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs34762184	0.88[CEU][hapmap]
rs35053615	0.80[EUR][1000 genomes]
rs35198275	0.80[EUR][1000 genomes]
rs35335661	0.80[EUR][1000 genomes]
rs35684775	0.80[EUR][1000 genomes]
rs35829757	0.80[EUR][1000 genomes]
rs35986136	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs36059704	0.80[EUR][1000 genomes]
rs4688719	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688720	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58432784	0.80[EUR][1000 genomes]
rs628081	0.83[CEU][hapmap]
rs6786523	0.83[CEU][hapmap]
rs6788459	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792502	0.83[CEU][hapmap]
rs6807916	0.88[CEU][hapmap]
rs71326932	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71326934	0.80[EUR][1000 genomes]
rs734767	0.94[CEU][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs73835511	0.80[EUR][1000 genomes]
rs743756	0.94[CEU][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs743757	0.94[CEU][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs743857	0.94[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7613931	0.80[EUR][1000 genomes]
rs762895	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs762897	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs762898	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs763030	0.83[CEU][hapmap]
rs8180034	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916217	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs929047	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9835537	0.94[CEU][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs9867588	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv998611	chr3:50519293-50526732	Weak transcription Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6787890	APEH	cis	cerebellum	SCAN
rs6787890	HYAL2	cis	parietal	SCAN
rs6787890	PARP3	cis	parietal	SCAN
rs6787890	TRAIP	cis	parietal	SCAN
rs6787890	CAMP	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50492600-50528400	Weak transcription	Gastric	stomach
2	chr3:50502800-50520800	Weak transcription	Brain Anterior Caudate	brain
3	chr3:50512000-50523000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:50512600-50524200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:50513000-50527400	Weak transcription	Right Atrium	heart
6	chr3:50517000-50520200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:50517200-50520200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:50518000-50520400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr3:50518000-50520400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:50518000-50520800	Enhancers	Fetal Muscle Leg	muscle
11	chr3:50518000-50521600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:50518000-50522000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:50518400-50520200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:50518400-50520200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr3:50518400-50520200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:50518400-50520200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:50518400-50520200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr3:50518400-50521000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr3:50518600-50520200	Enhancers	Primary T cells from cord blood	blood
20	chr3:50518600-50520200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:50518600-50520400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr3:50518600-50520400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr3:50518600-50522000	Enhancers	Lung	lung
24	chr3:50518600-50523600	Enhancers	Fetal Muscle Trunk	muscle
25	chr3:50518800-50521800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:50519000-50520600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:50519600-50520800	Enhancers	Spleen	Spleen
28	chr3:50519800-50520800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:50519800-50524600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:50520000-50520200	Enhancers	Brain Germinal Matrix	brain
31	chr3:50520000-50520200	Enhancers	Fetal Thymus	thymus
32	chr3:50520000-50520200	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr3:50520000-50524600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:50520000-50524800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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