Variant report

Variant	rs3108548
Chromosome Location	chr19:37050782-37050783
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37050035..37052914-chr19:37064018..37065875,2	K562	blood:
2	chr19:37050035..37052115-chr19:37063712..37065875,2	K562	blood:

Variant related genes	Relation type
ENSG00000186020	Chromatin interaction
ENSG00000233527	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10411411	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1053064	0.90[EUR][1000 genomes]
rs12162275	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12973307	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278168	0.82[TSI][hapmap]
rs2912401	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912402	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912406	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912416	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2912417	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967424	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967455	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3096621	0.94[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3096626	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108169	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108170	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108175	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108180	0.88[EUR][1000 genomes]
rs3108198	0.87[EUR][1000 genomes]
rs3108199	0.84[EUR][1000 genomes]
rs3108200	0.87[EUR][1000 genomes]
rs3108207	0.95[CEU][hapmap];0.94[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs3108210	0.82[TSI][hapmap]
rs3108213	0.87[EUR][1000 genomes]
rs3108547	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108553	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108554	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108558	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108571	0.87[EUR][1000 genomes]
rs3108578	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs3108581	0.87[EUR][1000 genomes]
rs3108587	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3108595	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108599	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108601	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108611	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3111543	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3111545	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3111546	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3745779	0.82[TSI][hapmap]
rs71337534	0.81[EUR][1000 genomes]
rs7254978	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[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8112546	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826986	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	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
7	nsv1056134	chr19:37022039-37056943	Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
8	esv3334779	chr19:37050161-37076919	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription 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	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3108548	GGN	cis	cerebellum	SCAN
rs3108548	RYR1	cis	cerebellum	SCAN
rs3108548	NKPD1	cis	cerebellum	SCAN
rs3108548	SARS2	cis	cerebellum	SCAN
rs3108548	PSG8	cis	cerebellum	SCAN
rs3108548	FBXO17	cis	cerebellum	SCAN
rs3108548	CIC	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37021400-37061600	ZNF genes & repeats	Liver	Liver
2	chr19:37022800-37061200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:37023000-37061800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:37023200-37060200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
5	chr19:37023200-37061600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:37023400-37060000	ZNF genes & repeats	Fetal Lung	lung
7	chr19:37023400-37062000	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:37023400-37063000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:37023600-37061000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
10	chr19:37023800-37057800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:37023800-37058200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:37023800-37058200	ZNF genes & repeats	Dnd41	blood
13	chr19:37023800-37061600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:37025400-37052400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr19:37025600-37053000	ZNF genes & repeats	Brain Anterior Caudate	brain
16	chr19:37025600-37061000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
17	chr19:37025600-37062800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:37025800-37060200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
19	chr19:37027400-37054400	ZNF genes & repeats	Brain Hippocampus Middle	brain
20	chr19:37028600-37050800	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr19:37028600-37055000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr19:37028600-37061800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
23	chr19:37028800-37054400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
24	chr19:37029000-37060000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
25	chr19:37031400-37056800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
26	chr19:37031400-37057800	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr19:37033400-37051000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:37034000-37054000	ZNF genes & repeats	A549	lung
29	chr19:37034000-37063000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:37034200-37052800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr19:37034200-37059600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
32	chr19:37034400-37052600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
33	chr19:37034800-37057200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
34	chr19:37036200-37059400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:37045600-37054400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
36	chr19:37047000-37058800	Weak transcription	K562	blood
37	chr19:37048000-37051800	Weak transcription	HSMMtube	muscle
38	chr19:37048400-37051600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr19:37048400-37062800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:37048800-37050800	Weak transcription	HSMM	muscle
41	chr19:37049600-37052800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
42	chr19:37049800-37052600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:37049800-37058000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
44	chr19:37049800-37061800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr19:37050000-37051000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:37050000-37051000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:37050000-37051000	ZNF genes & repeats	Brain Angular Gyrus	brain
48	chr19:37050000-37051000	ZNF genes & repeats	Brain Germinal Matrix	brain
49	chr19:37050000-37051200	ZNF genes & repeats	Small Intestine	intestine
50	chr19:37050000-37052200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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