Variant report

Variant	rs899349
Chromosome Location	chr3:140971176-140971177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140949417..140951197-chr3:140969315..140971449,2	MCF-7	breast:
2	chr3:140962275..140965128-chr3:140970545..140973245,4	K562	blood:
3	chr3:140966619..140969493-chr3:140970424..140973132,3	MCF-7	breast:
4	chr3:140968757..140971307-chr3:140972187..140974906,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11715472	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1511377	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1511386	0.82[EUR][1000 genomes]
rs1877219	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2169868	0.82[EUR][1000 genomes]
rs2311734	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4683398	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4683588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683592	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6439984	0.82[EUR][1000 genomes]
rs6439985	0.82[EUR][1000 genomes]
rs6439990	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6439993	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6803826	0.82[AMR][1000 genomes]
rs7629077	0.80[EUR][1000 genomes]
rs9289627	0.94[EUR][1000 genomes]
rs9841326	0.82[AMR][1000 genomes]
rs9878866	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

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

No data

Chromatin state (count:59 , 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	chr3:140957800-140973600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:140960000-140980000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:140961000-140978800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:140961200-140973600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:140961200-140985800	Weak transcription	Adipose Nuclei	Adipose
11	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
12	chr3:140961400-140974200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:140961400-140974200	Weak transcription	Brain Substantia Nigra	brain
14	chr3:140961400-140974400	Weak transcription	Placenta	Placenta
15	chr3:140961400-140983200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:140961600-140971400	Weak transcription	Fetal Brain Female	brain
17	chr3:140962000-140985800	Weak transcription	Brain Anterior Caudate	brain
18	chr3:140962200-140974200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:140962400-140977000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:140962400-140979200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:140962600-140971600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:140962600-140974200	Weak transcription	Spleen	Spleen
23	chr3:140962600-140974600	Weak transcription	Right Atrium	heart
24	chr3:140962600-140975000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:140962600-140978800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:140962600-140979600	Weak transcription	Fetal Intestine Large	intestine
27	chr3:140962600-140980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:140962800-140971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:140963400-140982800	Weak transcription	Brain Germinal Matrix	brain
30	chr3:140963600-140978800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:140964800-140978000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:140965400-140971600	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:140966000-140990200	Weak transcription	Psoas Muscle	Psoas
34	chr3:140966200-140974200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:140966200-140979600	Weak transcription	Pancreas	Pancrea
36	chr3:140968000-140976600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:140968200-140979000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:140968200-140990000	Weak transcription	Gastric	stomach
39	chr3:140968400-140982800	Weak transcription	Fetal Lung	lung
40	chr3:140968600-140971600	Weak transcription	Fetal Brain Male	brain
41	chr3:140968800-140974400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:140969200-140972200	Strong transcription	Fetal Stomach	stomach
43	chr3:140969200-140972600	Genic enhancers	Dnd41	blood
44	chr3:140969600-140974400	Weak transcription	Left Ventricle	heart
45	chr3:140969600-140974600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr3:140969800-140971600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:140970000-140972400	Strong transcription	Primary T cells from cord blood	blood
48	chr3:140970000-140974200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:140970200-140974000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:140970200-140974800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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