Variant report

Variant	rs2247798
Chromosome Location	chr19:43954915-43954916
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2599471	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2599472	0.94[ASW][hapmap];0.81[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2599474	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2682598	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv1060280	chr19:43866823-43959685	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv520852	chr19:43885085-43960114	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv579850	chr19:43885085-43960114	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1066231	chr19:43918840-43954915	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv579851	chr19:43920612-43955114	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv1061862	chr19:43925290-43954915	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv1058848	chr19:43925290-43957387	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv2501	chr19:43942581-43978424	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2247798	GIPR	cis	cerebellum	SCAN
rs2247798	BCL2L12	cis	parietal	SCAN
rs2247798	SIGLEC8	cis	cerebellum	SCAN
rs2247798	SNORD32A	cis	cerebellum	SCAN
rs2247798	KLC3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43944000-43956600	Weak transcription	Spleen	Spleen
2	chr19:43951200-43964800	Weak transcription	Esophagus	oesophagus
3	chr19:43951800-43959600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:43951800-43960000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr19:43952000-43956800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:43952600-43955000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:43954200-43955200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:43954600-43955000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:43954600-43955000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr19:43954600-43955200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr19:43954600-43955400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:43954600-43955400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr19:43954600-43957000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:43954800-43955200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr19:43954800-43955200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:43954800-43955200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr19:43954800-43955200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:43954800-43955200	Enhancers	Duodenum Mucosa	Duodenum
19	chr19:43954800-43955200	Enhancers	Fetal Thymus	thymus
20	chr19:43954800-43955200	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr19:43954800-43955200	Enhancers	NH-A	brain
22	chr19:43954800-43955200	Enhancers	Osteobl	bone
23	chr19:43954800-43955400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:43954800-43955400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:43954800-43955400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr19:43954800-43955400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:43954800-43955400	Enhancers	HMEC	breast
28	chr19:43954800-43955400	Enhancers	NHEK	skin

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