Variant report

Variant	rs2899888
Chromosome Location	chr14:39889759-39889760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39882950..39886541-chr14:39887581..39892204,4	MCF-7	breast:
2	chr14:39888039..39890423-chr14:39893808..39896011,2	MCF-7	breast:
3	chr14:39887184..39890386-chr14:39899843..39902826,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165355	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12587625	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12588110	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12588175	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12588483	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12590172	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12880644	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12882250	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12886769	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12897960	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1950336	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1950338	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207291	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2274395	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2415549	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2415550	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2899889	0.80[ASN][1000 genomes]
rs34432449	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34649642	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35459433	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35553183	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35693868	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36010374	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3814860	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4899245	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4899277	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4899278	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4902598	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902599	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4902622	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4902636	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4902637	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4902648	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4902665	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902676	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56046902	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71407788	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71407789	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7140983	0.85[EUR][1000 genomes]
rs7152341	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7152935	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7153413	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7161403	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72675487	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8003397	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8003621	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8006123	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8006321	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs910370	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs910371	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9332387	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39863400-39891600	Weak transcription	Small Intestine	intestine
2	chr14:39864600-39898800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr14:39865000-39891200	Weak transcription	Psoas Muscle	Psoas
4	chr14:39865000-39898200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr14:39869000-39895600	Weak transcription	Hela-S3	cervix
6	chr14:39882200-39895400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr14:39885200-39891400	Weak transcription	Gastric	stomach
8	chr14:39886000-39890800	Weak transcription	Fetal Brain Male	brain
9	chr14:39886000-39895600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:39886200-39890600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr14:39886200-39895600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr14:39886400-39892600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr14:39886400-39895600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr14:39886600-39890200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr14:39886600-39890200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr14:39886600-39890200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr14:39886600-39890800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr14:39886600-39890800	Weak transcription	Brain Angular Gyrus	brain
19	chr14:39886600-39891200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr14:39886600-39891200	Weak transcription	Lung	lung
21	chr14:39886600-39891200	Weak transcription	Ovary	ovary
22	chr14:39886600-39891200	Weak transcription	Right Ventricle	heart
23	chr14:39886600-39891400	Weak transcription	Aorta	Aorta
24	chr14:39886600-39891800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:39886600-39894000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr14:39886600-39894400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr14:39886600-39895600	Weak transcription	Fetal Lung	lung
28	chr14:39886600-39895800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr14:39886600-39895800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr14:39886600-39898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:39886600-39900000	Weak transcription	Esophagus	oesophagus
32	chr14:39886600-39900000	Weak transcription	Pancreas	Pancrea
33	chr14:39886800-39889800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr14:39886800-39890200	Weak transcription	Primary T cells from cord blood	blood
35	chr14:39886800-39890200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr14:39886800-39891200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr14:39886800-39892600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr14:39886800-39895600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr14:39886800-39895600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr14:39886800-39895600	Weak transcription	HepG2	liver
41	chr14:39886800-39895800	Weak transcription	Brain Anterior Caudate	brain
42	chr14:39886800-39895800	Weak transcription	Fetal Thymus	thymus
43	chr14:39886800-39895800	Weak transcription	Thymus	Thymus
44	chr14:39886800-39899200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr14:39886800-39899600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr14:39887000-39895800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:39887000-39899200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr14:39887200-39895400	Weak transcription	Dnd41	blood
49	chr14:39887200-39895600	Weak transcription	GM12878-XiMat	blood
50	chr14:39887600-39891200	Weak transcription	Fetal Intestine Small	intestine

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