Variant report

Variant	rs2292404
Chromosome Location	chr3:140985697-140985698
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	chr3:140984792..140987604-chr3:140994461..140996447,2	K562	blood:
2	chr3:140985576..140987715-chr3:140988575..140990710,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1026716	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs10935425	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10935427	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10935428	0.85[CEU][hapmap]
rs12486843	0.82[CEU][hapmap]
rs12488569	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13064327	0.89[EUR][1000 genomes]
rs13088065	0.81[AMR][1000 genomes]
rs1511375	0.90[EUR][1000 genomes]
rs1511379	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs1877223	0.82[AMR][1000 genomes]
rs6786821	0.81[CEU][hapmap];0.86[AMR][1000 genomes]
rs870400	0.87[EUR][1000 genomes]
rs9816975	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9819731	0.93[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9840622	0.83[AMR][1000 genomes];0.85[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:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140955400-140985800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:140961200-140985800	Weak transcription	Adipose Nuclei	Adipose
5	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
6	chr3:140962000-140985800	Weak transcription	Brain Anterior Caudate	brain
7	chr3:140966000-140990200	Weak transcription	Psoas Muscle	Psoas
8	chr3:140968200-140990000	Weak transcription	Gastric	stomach
9	chr3:140974800-140985800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:140974800-140987400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:140974800-140991400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:140975000-140985800	Weak transcription	Right Atrium	heart
13	chr3:140975000-140993400	Weak transcription	Lung	lung
14	chr3:140975000-140993400	Weak transcription	Spleen	Spleen
15	chr3:140975200-140991800	Weak transcription	Placenta	Placenta
16	chr3:140975400-140990200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:140975800-140993200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:140976400-140987200	Weak transcription	Fetal Brain Male	brain
19	chr3:140976600-140985800	Weak transcription	Fetal Heart	heart
20	chr3:140977800-140990000	Weak transcription	Liver	Liver
21	chr3:140978000-140998000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:140978200-140993600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:140978800-140986200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:140978800-140988000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:140978800-140993000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:140979000-141000800	Weak transcription	Fetal Kidney	kidney
27	chr3:140979000-141013200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:140979400-140986600	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:140979800-140992800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:140980000-140985800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:140980200-140985800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:140980200-140987600	Weak transcription	Pancreas	Pancrea
33	chr3:140980600-140986000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:140980800-141005600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:140981000-140998400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:140981200-141013200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:140981200-141013400	Weak transcription	Colonic Mucosa	Colon
38	chr3:140981400-141001000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:140981600-140992000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:140981600-140993200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:140982800-140986000	Strong transcription	Fetal Intestine Small	intestine
42	chr3:140983000-140992000	Weak transcription	Brain Angular Gyrus	brain
43	chr3:140983200-140990000	Weak transcription	Fetal Intestine Large	intestine
44	chr3:140983600-140985800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr3:140983600-141021600	Weak transcription	Esophagus	oesophagus
46	chr3:140983800-140993000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:140984000-140997400	Weak transcription	Fetal Brain Female	brain
48	chr3:140984200-141000800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:140984400-140985800	Weak transcription	Left Ventricle	heart
50	chr3:140984400-140985800	Weak transcription	Monocytes-CD14+_RO01746	blood

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