Variant report

Variant	rs3108581
Chromosome Location	chr19:37217437-37217438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10411411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1053064	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12162275	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12973307	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12981751	0.83[CEU][hapmap];0.88[AFR][1000 genomes]
rs2278168	0.87[TSI][hapmap]
rs2385640	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2462576	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2912401	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2912402	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs2912406	0.88[EUR][1000 genomes]
rs2912416	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2912417	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2967424	0.88[EUR][1000 genomes]
rs2967455	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967470	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3096621	0.88[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3096626	0.82[EUR][1000 genomes]
rs3108169	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108170	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108175	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108180	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108198	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108199	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108200	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108207	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108210	0.87[TSI][hapmap]
rs3108213	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108220	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3108547	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108548	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs3108551	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108553	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108554	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108558	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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108561	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108571	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108582	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3108587	0.84[EUR][1000 genomes]
rs3108588	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3108595	0.88[EUR][1000 genomes]
rs3108599	0.86[EUR][1000 genomes]
rs3108601	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108611	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108612	0.82[TSI][hapmap]
rs3111543	0.88[EUR][1000 genomes]
rs3111545	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3111546	0.88[EUR][1000 genomes]
rs3745779	0.87[TSI][hapmap]
rs71337534	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7254978	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];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8112546	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs826979	0.92[ASN][1000 genomes]
rs826980	0.93[ASN][1000 genomes]
rs826986	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs865448	0.92[AFR][1000 genomes];0.97[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	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS 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	27 gene(s)	inside rSNPs	diseases
8	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv470139	chr19:37171201-37264190	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	esv3517005	chr19:37193712-37364110	Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	esv3517004	chr19:37193762-37363960	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	esv3517006	chr19:37193762-37363960	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv911649	chr19:37203249-37257192	ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
15	esv3508979	chr19:37208161-37252433	ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
16	esv3508980	chr19:37208161-37252433	ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3108581	RYR1	cis	cerebellum	SCAN
rs3108581	ZNF529	Cis_1M	lymphoblastoid	RTeQTL
rs3108581	ZFP36	cis	cerebellum	SCAN
rs3108581	CIC	cis	cerebellum	SCAN
rs3108581	FBXO17	cis	cerebellum	SCAN
rs3108581	GGN	cis	cerebellum	SCAN
rs3108581	SARS2	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37194000-37254000	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:37194400-37219400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:37194400-37221400	ZNF genes & repeats	Dnd41	blood
4	chr19:37194400-37253800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:37194600-37220800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr19:37194600-37227000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:37194600-37258800	ZNF genes & repeats	Liver	Liver
8	chr19:37197000-37226400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:37206600-37217800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
10	chr19:37212800-37219000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:37212800-37219000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:37212800-37219000	ZNF genes & repeats	Left Ventricle	heart
13	chr19:37214400-37218400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:37214600-37219200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:37215000-37219000	Weak transcription	Fetal Heart	heart
16	chr19:37215800-37219200	ZNF genes & repeats	Fetal Brain Female	brain
17	chr19:37216200-37219000	ZNF genes & repeats	Right Ventricle	heart
18	chr19:37216200-37219200	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr19:37216200-37220800	ZNF genes & repeats	Brain Anterior Caudate	brain
20	chr19:37216200-37221000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:37216200-37222000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
22	chr19:37216200-37226600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
23	chr19:37216200-37228600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
24	chr19:37216400-37217800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:37216400-37217800	ZNF genes & repeats	Brain Angular Gyrus	brain
26	chr19:37216400-37217800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
27	chr19:37216400-37217800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
28	chr19:37216400-37217800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
29	chr19:37216400-37219000	ZNF genes & repeats	Aorta	Aorta
30	chr19:37216400-37219000	ZNF genes & repeats	Placenta	Placenta
31	chr19:37216400-37219400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:37216400-37221000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:37216400-37221400	ZNF genes & repeats	Brain Hippocampus Middle	brain
34	chr19:37216600-37217800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:37216600-37217800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:37216600-37219400	ZNF genes & repeats	Colon Smooth Muscle	Colon
37	chr19:37216600-37219600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr19:37216800-37217800	ZNF genes & repeats	Brain Substantia Nigra	brain
39	chr19:37216800-37217800	ZNF genes & repeats	A549	lung
40	chr19:37216800-37225200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
41	chr19:37216800-37232400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:37217000-37217800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
43	chr19:37217000-37219200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
44	chr19:37217000-37219400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
45	chr19:37217000-37219400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
46	chr19:37217000-37220800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
47	chr19:37217000-37220800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
48	chr19:37217200-37217600	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:37217200-37217600	ZNF genes & repeats	Psoas Muscle	Psoas
50	chr19:37217200-37217800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood

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