Variant report

Variant	rs2682562
Chromosome Location	chr19:44040997-44040998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11407	1.00[ASW][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2021092	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs25484	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2599442	0.90[ASW][hapmap]
rs2599459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2599464	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2682552	0.93[CEU][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2682560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2682587	1.00[ASW][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682588	0.80[EUR][1000 genomes]
rs2854495	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2854496	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2854498	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2854502	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2854505	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2854510	0.82[ASW][hapmap];0.93[CEU][hapmap];0.85[GIH][hapmap];0.88[EUR][1000 genomes]
rs304729	0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs304730	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3213283	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3213285	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3213289	0.88[EUR][1000 genomes]
rs3213332	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3213370	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs939460	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers 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	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
12	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv912107	chr19:44030998-44055726	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2682562	SLC8A2	cis	cerebellum	SCAN
rs2682562	STRN4	cis	cerebellum	SCAN
rs2682562	ZNF575	cis	Adipose Subcutaneous	GTEx
rs2682562	PHLDB3	cis	lesional skin	skin_eQTL
rs2682562	PHLDB3	cis	normal skin	skin_eQTL
rs2682562	NANOS2	cis	parietal	SCAN
rs2682562	PIH1D1	cis	cerebellum	SCAN
rs2682562	ZNF575	cis	Nerve Tibial	GTEx
rs2682562	ZNF575	cis	Skin Sun Exposed Lower leg	GTEx
rs2682562	SNRPD2	cis	parietal	SCAN
rs2682562	XRCC1	cis	lymphoblastoid	seeQTL
rs2682562	ZNF575	cis	Artery Tibial	GTEx
rs2682562	BCAT2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44038000-44042400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr19:44038000-44046800	Weak transcription	Small Intestine	intestine
3	chr19:44038200-44041400	Weak transcription	Primary T cells from cord blood	blood
4	chr19:44038200-44042400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:44038200-44042600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:44038200-44042600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:44038200-44042600	Weak transcription	HepG2	liver
8	chr19:44038200-44042600	Weak transcription	HSMMtube	muscle
9	chr19:44038400-44041800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:44038400-44042600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:44038400-44043000	Weak transcription	GM12878-XiMat	blood
12	chr19:44038400-44043200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:44038400-44043400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:44038600-44041000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:44038600-44041800	Weak transcription	Ovary	ovary
16	chr19:44038600-44042000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr19:44038600-44042200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:44038600-44042400	Weak transcription	Left Ventricle	heart
19	chr19:44038600-44042600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr19:44038600-44042600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:44038600-44042600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr19:44038600-44043400	Weak transcription	NHEK	skin
23	chr19:44038600-44054000	Weak transcription	Psoas Muscle	Psoas
24	chr19:44038800-44041600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr19:44038800-44041600	Weak transcription	Fetal Intestine Large	intestine
26	chr19:44038800-44042400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr19:44038800-44042400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr19:44038800-44042400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr19:44038800-44042400	Weak transcription	HSMM	muscle
30	chr19:44038800-44042400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr19:44038800-44042600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:44038800-44042600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr19:44038800-44042600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr19:44038800-44042600	Weak transcription	Fetal Kidney	kidney
35	chr19:44038800-44042600	Weak transcription	K562	blood
36	chr19:44038800-44042800	Weak transcription	Primary B cells from cord blood	blood
37	chr19:44038800-44044400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr19:44038800-44046800	Weak transcription	Esophagus	oesophagus
39	chr19:44038800-44055800	Weak transcription	Stomach Mucosa	stomach
40	chr19:44039000-44041400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:44039000-44041600	Weak transcription	Adipose Nuclei	Adipose
42	chr19:44039000-44041600	Weak transcription	Fetal Thymus	thymus
43	chr19:44039000-44041800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:44039000-44041800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr19:44039000-44042200	Weak transcription	A549	lung
46	chr19:44039000-44042400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:44039000-44042400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr19:44039000-44042400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr19:44039000-44042600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr19:44039000-44042600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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