Variant report

Variant	rs1623097
Chromosome Location	chr19:37473242-37473243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10401212	0.93[JPT][hapmap]
rs10401417	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404981	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10405238	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10405984	0.86[CEU][hapmap]
rs10407712	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408534	0.91[ASN][1000 genomes]
rs10408951	0.92[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];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10411037	0.81[EUR][1000 genomes]
rs10411251	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10411931	0.86[CEU][hapmap];0.87[MEX][hapmap]
rs10412863	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416960	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10419845	0.81[EUR][1000 genomes]
rs10420859	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424100	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12710052	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12977971	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981965	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13345489	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617883	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1623796	0.85[JPT][hapmap]
rs1624293	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628959	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1644664	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1644701	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1644702	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1644704	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1667351	0.86[JPT][hapmap]
rs1667357	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667359	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16971771	0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs16971772	0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs16971850	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17639910	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17707101	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595552	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28495495	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28542490	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555503	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608841	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655720	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34791663	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35881914	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816390	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816391	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[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	0.92[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs4806376	0.83[ASN][1000 genomes]
rs4806377	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4806380	0.86[CEU][hapmap];0.87[MEX][hapmap]
rs4806386	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs543518	0.81[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs62109879	0.81[EUR][1000 genomes]
rs62113193	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62115612	0.83[ASN][1000 genomes]
rs62115615	0.85[ASN][1000 genomes]
rs6510572	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71266562	0.94[ASN][1000 genomes]
rs71356024	0.98[ASN][1000 genomes]
rs7249013	0.87[ASN][1000 genomes]
rs7250498	0.94[ASN][1000 genomes]
rs7251087	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252797	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8112709	0.89[EUR][1000 genomes]
rs9304878	0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap]
rs997516	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1623097	FLJ32191	cis	multi-tissue	Pritchard
rs1623097	MEGF8	cis	cerebellum	SCAN
rs1623097	EXOSC5	cis	cerebellum	SCAN
rs1623097	APOC4	cis	cerebellum	SCAN
rs1623097	PSMC4	cis	parietal	SCAN
rs1623097	ITPKC	cis	cerebellum	SCAN
rs1623097	ZNF420	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37464800-37473600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:37464800-37482000	Weak transcription	HSMMtube	muscle
3	chr19:37465000-37473600	Weak transcription	Small Intestine	intestine
4	chr19:37465000-37487200	Weak transcription	Placenta	Placenta
5	chr19:37465200-37473600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:37465200-37476800	Weak transcription	NH-A	brain
7	chr19:37465200-37481800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:37465200-37482600	Weak transcription	Right Ventricle	heart
9	chr19:37465400-37473800	Weak transcription	Spleen	Spleen
10	chr19:37465400-37483400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:37465400-37483600	Weak transcription	Fetal Heart	heart
12	chr19:37465600-37474200	Weak transcription	Colonic Mucosa	Colon
13	chr19:37465600-37482400	Weak transcription	Fetal Kidney	kidney
14	chr19:37467000-37474600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:37468400-37474400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:37468400-37474400	ZNF genes & repeats	Liver	Liver
17	chr19:37468800-37473400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:37468800-37487800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:37469000-37474000	Weak transcription	NHDF-Ad	bronchial
20	chr19:37469200-37473800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr19:37469400-37479200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr19:37469800-37474000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:37469800-37474200	Weak transcription	Lung	lung
24	chr19:37469800-37477600	Weak transcription	Aorta	Aorta
25	chr19:37470400-37477000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:37470400-37477600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:37470600-37482200	Weak transcription	Psoas Muscle	Psoas
28	chr19:37471600-37474400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
29	chr19:37471800-37476400	Weak transcription	Primary B cells from cord blood	blood
30	chr19:37471800-37478000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:37471800-37480400	Weak transcription	Gastric	stomach
32	chr19:37471800-37480600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr19:37471800-37482000	Weak transcription	Left Ventricle	heart
34	chr19:37471800-37482600	Weak transcription	Brain Substantia Nigra	brain
35	chr19:37472000-37473400	Strong transcription	Ovary	ovary
36	chr19:37472000-37473800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:37472000-37474200	Weak transcription	Adipose Nuclei	Adipose
38	chr19:37472000-37474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:37472000-37476600	Weak transcription	Fetal Stomach	stomach
40	chr19:37472000-37477000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:37472000-37477600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:37472000-37477600	Weak transcription	Fetal Brain Female	brain
43	chr19:37472000-37477800	Weak transcription	Brain Hippocampus Middle	brain
44	chr19:37472000-37479200	Weak transcription	Pancreas	Pancrea
45	chr19:37472000-37479400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr19:37472000-37481600	Weak transcription	Brain Anterior Caudate	brain
47	chr19:37472000-37483600	Weak transcription	Osteobl	bone
48	chr19:37472200-37474000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:37472200-37475400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:37472200-37475400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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