Variant report

Variant	rs3826849
Chromosome Location	chr19:37878856-37878857
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	chr19:37855409..37858293-chr19:37876540..37879521,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11083427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1128327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11673646	0.85[YRI][hapmap]
rs12151218	0.85[EUR][1000 genomes]
rs12151280	0.90[JPT][hapmap]
rs12459637	0.85[YRI][hapmap]
rs12459975	0.85[EUR][1000 genomes]
rs12461941	0.84[EUR][1000 genomes]
rs12462271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs12986074	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12986146	0.90[JPT][hapmap]
rs17243355	0.89[EUR][1000 genomes]
rs17303301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2279150	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3745764	1.00[ASW][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong 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	13 gene(s)	inside rSNPs	diseases
5	nsv1058788	chr19:37857748-37899157	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv579464	chr19:37858660-37881556	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv579465	chr19:37868552-37917692	ZNF genes & repeats Strong transcription Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3826849	FOSB	cis	cerebellum	SCAN
rs3826849	KIAA0961	cis	multi-tissue	Pritchard
rs3826849	CATSPERG	cis	parietal	SCAN
rs3826849	PSMC4	cis	parietal	SCAN
rs3826849	MRPS12	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37864000-37882000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:37864000-37882000	ZNF genes & repeats	Liver	Liver
3	chr19:37864400-37880600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:37864400-37880800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr19:37864600-37880600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
6	chr19:37864600-37890600	ZNF genes & repeats	Adipose Nuclei	Adipose
7	chr19:37865000-37880600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
8	chr19:37865400-37880600	ZNF genes & repeats	Primary T cells from cord blood	blood
9	chr19:37868000-37880400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
10	chr19:37868000-37880800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:37868000-37881000	ZNF genes & repeats	A549	lung
12	chr19:37868000-37882000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
13	chr19:37868000-37882200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr19:37868000-37886600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr19:37868200-37881000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
16	chr19:37868200-37881600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr19:37868200-37882000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
18	chr19:37868400-37880000	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr19:37869400-37881600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
20	chr19:37869600-37880800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:37869800-37881600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr19:37870000-37880600	ZNF genes & repeats	Ovary	ovary
23	chr19:37870000-37881600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
24	chr19:37870000-37881800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:37870000-37882200	ZNF genes & repeats	Colon Smooth Muscle	Colon
26	chr19:37871000-37880600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
27	chr19:37871000-37881600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
28	chr19:37871200-37882800	ZNF genes & repeats	Psoas Muscle	Psoas
29	chr19:37872000-37880600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
30	chr19:37872200-37880600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
31	chr19:37872800-37880200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:37872800-37880400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:37872800-37880600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:37872800-37880600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
35	chr19:37872800-37882200	ZNF genes & repeats	Fetal Brain Female	brain
36	chr19:37873000-37880200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:37873000-37880600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr19:37873000-37880600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
39	chr19:37873000-37880600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
40	chr19:37873000-37880800	ZNF genes & repeats	Colonic Mucosa	Colon
41	chr19:37873000-37881400	ZNF genes & repeats	Aorta	Aorta
42	chr19:37873000-37881600	ZNF genes & repeats	Left Ventricle	heart
43	chr19:37873400-37880600	ZNF genes & repeats	Small Intestine	intestine
44	chr19:37873600-37880600	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr19:37873600-37882000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:37874000-37880800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
47	chr19:37874000-37880800	ZNF genes & repeats	Primary B cells from cord blood	blood
48	chr19:37874000-37881800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:37874000-37882200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
50	chr19:37874400-37881600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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