Variant report

Variant	rs3899404
Chromosome Location	chr14:39508746-39508747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39504261..39505866-chr14:39507926..39509842,2	K562	blood:
2	chr14:39507492..39510436-chr14:39510983..39512776,2	MCF-7	breast:
3	chr14:39506080..39508862-chr14:39528355..39530994,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10132034	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10132953	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10149829	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1015532	0.81[ASN][1000 genomes]
rs1040837	0.81[ASN][1000 genomes]
rs11157046	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12434607	0.82[EUR][1000 genomes]
rs12895329	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1950509	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1951221	0.81[ASN][1000 genomes]
rs1955917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1957061	0.81[ASN][1000 genomes]
rs1957062	0.81[ASN][1000 genomes]
rs1957063	0.81[ASN][1000 genomes]
rs1964842	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2038357	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2064959	0.81[ASN][1000 genomes]
rs2082637	0.83[AFR][1000 genomes]
rs2180214	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2180217	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2180792	0.87[AFR][1000 genomes]
rs2252040	0.87[AFR][1000 genomes]
rs4290398	0.82[AFR][1000 genomes]
rs4616209	0.85[EUR][1000 genomes]
rs4899125	0.81[ASN][1000 genomes]
rs4899126	0.81[ASN][1000 genomes]
rs4899139	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4899140	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902294	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902402	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4902419	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6571888	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6571889	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6571890	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6571891	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6571894	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6571895	0.84[AMR][1000 genomes]
rs6571896	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7147760	0.83[EUR][1000 genomes]
rs7154585	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7157204	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs761804	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs761806	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs761807	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8003194	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8003485	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8003807	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8010111	0.87[AFR][1000 genomes]
rs8011855	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8012178	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8014021	0.87[ASN][1000 genomes]
rs8014255	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs8014677	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9322993	0.87[EUR][1000 genomes]
rs9671927	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs970623	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs975591	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39495400-39518200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:39495600-39509800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:39495800-39516000	Weak transcription	Stomach Mucosa	stomach
4	chr14:39496000-39514800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:39496000-39520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr14:39497400-39518000	Strong transcription	HSMM	muscle
7	chr14:39497400-39519200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr14:39497800-39520400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr14:39497800-39521200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr14:39498000-39510000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr14:39498000-39518400	Strong transcription	Osteobl	bone
12	chr14:39498000-39518600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr14:39498000-39524200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr14:39498200-39509400	Weak transcription	Fetal Brain Male	brain
15	chr14:39498200-39510200	Strong transcription	Placenta	Placenta
16	chr14:39498200-39519400	Strong transcription	NH-A	brain
17	chr14:39498200-39524200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr14:39498200-39524400	Strong transcription	Fetal Intestine Large	intestine
19	chr14:39498400-39520000	Strong transcription	HepG2	liver
20	chr14:39498400-39524800	Weak transcription	K562	blood
21	chr14:39498600-39510000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr14:39498600-39518000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr14:39498600-39519600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr14:39498600-39524000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr14:39498600-39524800	Strong transcription	Adipose Nuclei	Adipose
26	chr14:39499000-39510200	Strong transcription	NHDF-Ad	bronchial
27	chr14:39499000-39510400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:39499000-39510400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr14:39499000-39510400	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr14:39499000-39523200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr14:39499000-39523600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr14:39499000-39524200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr14:39499000-39524800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr14:39499000-39524800	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr14:39499000-39525000	Strong transcription	Liver	Liver
36	chr14:39499600-39524600	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr14:39499800-39509000	Weak transcription	Brain Substantia Nigra	brain
38	chr14:39500000-39512600	Weak transcription	Aorta	Aorta
39	chr14:39500000-39519800	Weak transcription	Pancreas	Pancrea
40	chr14:39500000-39521000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr14:39500000-39522800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr14:39500000-39524400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr14:39500000-39524800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr14:39500000-39525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr14:39500200-39509600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr14:39500200-39515200	Weak transcription	Lung	lung
47	chr14:39500200-39515800	Weak transcription	Esophagus	oesophagus
48	chr14:39500200-39518600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr14:39500200-39519400	Weak transcription	Gastric	stomach
50	chr14:39500200-39523000	Weak transcription	Spleen	Spleen

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