Variant report

Variant	rs1628959
Chromosome Location	chr19:37490376-37490377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10401380	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10401417	0.81[EUR][1000 genomes]
rs10401561	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10402050	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10404069	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10404973	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10404981	0.86[CEU][hapmap]
rs10405238	0.85[EUR][1000 genomes]
rs10407014	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10407224	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10407265	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10407712	0.82[EUR][1000 genomes]
rs10408199	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10410594	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10410905	0.87[EUR][1000 genomes]
rs10411037	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10411176	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10412236	0.83[EUR][1000 genomes]
rs10413101	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10414107	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10414227	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10416960	0.85[CEU][hapmap]
rs10417545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10418314	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10419174	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10419845	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10420859	0.83[EUR][1000 genomes]
rs10422428	0.87[EUR][1000 genomes]
rs10424841	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10426093	0.85[EUR][1000 genomes]
rs11084873	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12972146	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12975706	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12978093	0.88[EUR][1000 genomes]
rs12981965	0.80[CEU][hapmap]
rs12983153	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs13346284	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1551025	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1617883	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1623097	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1624293	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1644664	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1644701	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1644702	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1644704	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1667357	0.99[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1667359	0.99[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16971850	0.86[CEU][hapmap]
rs17639910	0.81[EUR][1000 genomes]
rs17707101	0.85[CEU][hapmap]
rs2385412	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2595552	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs28462002	0.83[EUR][1000 genomes]
rs28631881	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34193103	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35080624	0.97[ASN][1000 genomes]
rs35522655	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35655645	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3816391	0.85[CEU][hapmap]
rs4805198	0.87[EUR][1000 genomes]
rs4805207	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4805208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4806406	0.87[EUR][1000 genomes]
rs4806414	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs62108899	0.84[EUR][1000 genomes]
rs62109879	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6510583	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7246473	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7247758	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7249696	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7252797	0.99[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7259878	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8101338	0.88[EUR][1000 genomes]
rs8107654	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9749562	0.91[ASN][1000 genomes]
rs997516	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv911653	chr19:37482151-37556673	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS 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	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1628959	FLJ32191	cis	multi-tissue	Pritchard
rs1628959	ZNF420	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37484400-37490600	Weak transcription	Stomach Mucosa	stomach
2	chr19:37488200-37490800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:37488200-37498200	Weak transcription	Fetal Heart	heart
4	chr19:37488400-37498000	Weak transcription	Placenta	Placenta
5	chr19:37488600-37490800	Weak transcription	Fetal Intestine Large	intestine
6	chr19:37488600-37491000	Weak transcription	Pancreas	Pancrea
7	chr19:37488600-37491200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:37488600-37491600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr19:37488600-37493000	Weak transcription	Left Ventricle	heart
10	chr19:37488600-37495200	Weak transcription	Right Ventricle	heart
11	chr19:37488600-37498200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:37488600-37498200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr19:37488600-37498400	Weak transcription	Brain Germinal Matrix	brain
14	chr19:37488600-37498400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:37488800-37491600	Weak transcription	Fetal Brain Male	brain
16	chr19:37488800-37492000	Weak transcription	Fetal Lung	lung
17	chr19:37489000-37490400	Weak transcription	Fetal Stomach	stomach
18	chr19:37489000-37491000	Weak transcription	Colon Smooth Muscle	Colon
19	chr19:37489000-37491600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr19:37489000-37491600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr19:37489000-37491800	Weak transcription	Brain Hippocampus Middle	brain
22	chr19:37489000-37493600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:37489000-37497800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:37489000-37498200	Weak transcription	Brain Angular Gyrus	brain
25	chr19:37489000-37498200	Weak transcription	Brain Substantia Nigra	brain
26	chr19:37489000-37498200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr19:37489200-37492000	Weak transcription	Fetal Muscle Leg	muscle
28	chr19:37489200-37495000	Weak transcription	Fetal Brain Female	brain

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