Variant report

Variant	rs17707101
Chromosome Location	chr19:37461850-37461851
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10401212	0.93[JPT][hapmap]
rs10401417	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10405238	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10405984	0.86[CEU][hapmap]
rs10407712	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408534	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10408951	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs10409206	0.86[ASN][1000 genomes]
rs10410594	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10411037	0.82[AFR][1000 genomes]
rs10411251	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10411931	0.86[CEU][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.81[YRI][hapmap]
rs10412863	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10418314	0.91[YRI][hapmap]
rs10419174	0.88[YRI][hapmap]
rs10419845	0.86[AFR][1000 genomes]
rs10420859	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424100	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10424841	0.87[YRI][hapmap]
rs11084873	0.88[YRI][hapmap]
rs12710052	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12977971	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13345489	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551025	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1623097	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1623796	0.85[JPT][hapmap]
rs1624293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1644664	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1644701	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1667351	0.86[JPT][hapmap]
rs1667357	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667359	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16971771	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs16971772	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs16971850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17639910	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595552	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28495495	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28542490	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555503	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608841	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655720	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34791663	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35080624	0.81[EUR][1000 genomes]
rs35881914	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816390	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3955478	0.93[JPT][hapmap]
rs4805189	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs4805190	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs4806376	0.83[ASN][1000 genomes]
rs4806377	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4806380	0.92[ASW][hapmap];0.86[CEU][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4806383	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4806386	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs543518	0.81[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs62109879	0.83[AFR][1000 genomes]
rs62113193	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62115612	0.83[ASN][1000 genomes]
rs62115615	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6510572	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71266562	0.94[ASN][1000 genomes]
rs71356024	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7249013	0.87[ASN][1000 genomes]
rs7250498	0.94[ASN][1000 genomes]
rs7251087	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252797	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8107654	0.87[EUR][1000 genomes]
rs8112709	1.00[EUR][1000 genomes]
rs9304878	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap]
rs997516	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv523848	chr19:37357289-37487632	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
14	nsv833818	chr19:37427808-37602800	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
15	nsv579463	chr19:37437106-37488055	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
16	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
17	esv3322425	chr19:37458912-37463110	Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17707101	MEGF8	cis	cerebellum	SCAN
rs17707101	EXOSC5	cis	cerebellum	SCAN
rs17707101	ITPKC	cis	cerebellum	SCAN
rs17707101	APOC4	cis	cerebellum	SCAN
rs17707101	PSMC4	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37447800-37463400	Weak transcription	Left Ventricle	heart
2	chr19:37450800-37463200	Weak transcription	Brain Anterior Caudate	brain
3	chr19:37451600-37463400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:37452000-37463200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:37455400-37463200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:37455600-37463200	Weak transcription	Brain Substantia Nigra	brain
7	chr19:37455600-37463400	Weak transcription	Placenta	Placenta
8	chr19:37456200-37463200	Weak transcription	Fetal Stomach	stomach
9	chr19:37456400-37463200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr19:37456600-37463200	Weak transcription	Fetal Muscle Leg	muscle
11	chr19:37457600-37463200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr19:37457800-37463200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:37457800-37463200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr19:37458000-37463200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:37458000-37463400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:37458000-37463600	Weak transcription	Aorta	Aorta
17	chr19:37458000-37463600	Weak transcription	Gastric	stomach
18	chr19:37458000-37463600	Weak transcription	Ovary	ovary
19	chr19:37458000-37463600	Weak transcription	Spleen	Spleen
20	chr19:37458600-37463200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:37458800-37463400	Weak transcription	HSMMtube	muscle
22	chr19:37459000-37463200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr19:37459800-37463400	Weak transcription	Right Ventricle	heart
24	chr19:37460400-37463400	Weak transcription	Fetal Brain Female	brain
25	chr19:37460600-37463400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr19:37460600-37463400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr19:37460800-37463000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:37461000-37463600	Weak transcription	Liver	Liver
29	chr19:37461400-37463200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:37461400-37463400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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