Variant report

Variant	rs3826919
Chromosome Location	chr19:40449191-40449192
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FCGBP-1	chr19:40448563-40449473	NONHSAT066326
2	lnc-FCGBP-1	chr19:40449146-40449587	NONHSAT066327

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs170900	0.83[CEU][hapmap]
rs2231738	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234340	0.83[CEU][hapmap]
rs234365	0.83[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2355720	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs337780	0.83[CEU][hapmap]
rs3754	0.83[ASN][1000 genomes]
rs3760919	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3760923	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3786938	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs424365	0.83[CEU][hapmap];0.87[ASN][1000 genomes]
rs427461	0.83[CEU][hapmap];0.89[CHB][hapmap]
rs7249286	0.83[CEU][hapmap]
rs7249890	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8106269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8109718	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8109879	0.89[ASN][1000 genomes]
rs9749001	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv510766	chr19:40344356-40453018	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases
6	nsv978815	chr19:40443651-40449610	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40442000-40450400	Weak transcription	Brain Substantia Nigra	brain
2	chr19:40442400-40450400	Weak transcription	Lung	lung
3	chr19:40446600-40449200	Flanking Active TSS	Dnd41	blood
4	chr19:40446800-40451600	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr19:40446800-40453000	Enhancers	Fetal Intestine Large	intestine
6	chr19:40446800-40453000	Enhancers	Stomach Mucosa	stomach
7	chr19:40447000-40449200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:40447000-40449200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr19:40447000-40449800	Enhancers	Fetal Muscle Leg	muscle
10	chr19:40447000-40450400	Enhancers	Thymus	Thymus
11	chr19:40447000-40450800	Enhancers	Fetal Thymus	thymus
12	chr19:40447200-40449600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr19:40447200-40453000	Enhancers	Fetal Intestine Small	intestine
14	chr19:40447400-40449600	Weak transcription	Placenta	Placenta
15	chr19:40447400-40450200	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr19:40447400-40451200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr19:40447600-40451000	Weak transcription	Brain Hippocampus Middle	brain
18	chr19:40447600-40451400	Enhancers	Fetal Kidney	kidney
19	chr19:40447800-40449600	Enhancers	Duodenum Mucosa	Duodenum
20	chr19:40447800-40449600	Enhancers	A549	lung
21	chr19:40447800-40451600	Enhancers	Colonic Mucosa	Colon
22	chr19:40447800-40452800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:40447800-40457000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr19:40448000-40450000	Weak transcription	HMEC	breast
25	chr19:40448200-40453200	Enhancers	Primary B cells from peripheral blood	blood
26	chr19:40448400-40449200	Enhancers	Small Intestine	intestine
27	chr19:40448400-40449600	Enhancers	Primary T cells from cord blood	blood
28	chr19:40448400-40449600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr19:40448400-40449600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr19:40448400-40449600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr19:40448400-40449600	Weak transcription	Liver	Liver
32	chr19:40448400-40449600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr19:40448400-40450000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr19:40448400-40450200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr19:40448400-40450200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:40448400-40455600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:40448400-40457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:40448600-40449600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr19:40448600-40449600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr19:40448600-40450600	Enhancers	GM12878-XiMat	blood
41	chr19:40448600-40452400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:40448600-40453000	Enhancers	Primary B cells from cord blood	blood
43	chr19:40448800-40449800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr19:40449000-40449200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:40449000-40449200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr19:40449000-40449200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:40449000-40449200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:40449000-40449200	Enhancers	Gastric	stomach
49	chr19:40449000-40449200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr19:40449000-40449200	Enhancers	Spleen	Spleen

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