Variant report

Variant	rs3796259
Chromosome Location	chr3:140978921-140978922
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	chr3:140977766..140980226-chr3:141006718..141009392,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1026716	0.82[MKK][hapmap]
rs11713226	0.80[CEU][hapmap]
rs4461396	0.82[CEU][hapmap]
rs4683399	0.82[CEU][hapmap]
rs6769909	1.00[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6775902	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3796259	RBP2	cis	parietal	SCAN
rs3796259	TRPC1	cis	parietal	SCAN
rs3796259	ACPL2	cis	parietal	SCAN
rs3796259	ACPL2	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:140955200-140980600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr3:140955400-140985800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:140960000-140980000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:140961200-140985800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
9	chr3:140961400-140983200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:140962000-140985800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:140962400-140979200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:140962600-140979600	Weak transcription	Fetal Intestine Large	intestine
13	chr3:140962600-140980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:140963400-140982800	Weak transcription	Brain Germinal Matrix	brain
15	chr3:140966000-140990200	Weak transcription	Psoas Muscle	Psoas
16	chr3:140966200-140979600	Weak transcription	Pancreas	Pancrea
17	chr3:140968200-140979000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:140968200-140990000	Weak transcription	Gastric	stomach
19	chr3:140968400-140982800	Weak transcription	Fetal Lung	lung
20	chr3:140971000-140979000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr3:140972000-140979000	Weak transcription	Fetal Intestine Small	intestine
22	chr3:140972200-140979000	Weak transcription	Fetal Stomach	stomach
23	chr3:140973200-140979000	Enhancers	Fetal Thymus	thymus
24	chr3:140974800-140985800	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:140974800-140987400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:140974800-140991400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:140975000-140979200	Weak transcription	Brain Angular Gyrus	brain
28	chr3:140975000-140979400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:140975000-140979400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:140975000-140979800	Weak transcription	Brain Substantia Nigra	brain
31	chr3:140975000-140984800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:140975000-140985800	Weak transcription	Right Atrium	heart
33	chr3:140975000-140993400	Weak transcription	Lung	lung
34	chr3:140975000-140993400	Weak transcription	Spleen	Spleen
35	chr3:140975200-140980600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:140975200-140984400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:140975200-140984800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:140975200-140985000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:140975200-140991800	Weak transcription	Placenta	Placenta
40	chr3:140975400-140979000	Weak transcription	Right Ventricle	heart
41	chr3:140975400-140979400	Weak transcription	Left Ventricle	heart
42	chr3:140975400-140979600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:140975400-140980000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:140975400-140980600	Weak transcription	HSMM	muscle
45	chr3:140975400-140983400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:140975400-140990200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:140975800-140979200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:140975800-140979800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:140975800-140980000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:140975800-140983600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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