Variant report

Variant	rs17617289
Chromosome Location	chr14:39586605-39586606
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39580982..39585066-chr14:39586310..39589000,3	MCF-7	breast:
2	chr14:39582622..39586619-chr14:39638047..39642701,6	MCF-7	breast:
3	chr14:39582595..39584912-chr14:39586260..39591171,5	MCF-7	breast:
4	chr14:39586594..39589451-chr14:39598001..39600988,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182400	Chromatin interaction
ENSG00000092208	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12882909	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12883114	0.86[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12891260	0.83[ASN][1000 genomes]
rs12891438	0.83[ASN][1000 genomes]
rs12896384	0.83[ASN][1000 genomes]
rs12896963	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12897263	0.83[ASN][1000 genomes]
rs12897381	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12897593	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17616347	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17617123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17679493	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1884383	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1950508	0.86[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1980611	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1980612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1980613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2038359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2038360	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2144527	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs2273315	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2415533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2753596	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs28364834	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34328534	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34896803	0.83[ASN][1000 genomes]
rs34984050	0.83[ASN][1000 genomes]
rs35006421	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35114880	0.93[ASN][1000 genomes]
rs35270180	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35395604	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35412542	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35502984	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35534904	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35729735	0.83[ASN][1000 genomes]
rs35767652	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36057038	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55902358	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55993688	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57550673	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59881143	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60085216	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66488055	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67190795	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67849341	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67968129	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7140282	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7140321	0.93[ASN][1000 genomes]
rs71407778	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7145712	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7145856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7152392	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs715267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7157774	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8007028	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8007240	0.86[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8008726	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8011244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8011494	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8020013	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs8020321	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9743466	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9743749	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39583800-39588000	Weak transcription	Gastric	stomach
2	chr14:39583800-39626000	Weak transcription	Spleen	Spleen
3	chr14:39584000-39588000	Weak transcription	Lung	lung
4	chr14:39584000-39588200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:39584000-39590000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr14:39584000-39595000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr14:39584000-39615000	Weak transcription	Pancreas	Pancrea
8	chr14:39584000-39623600	Weak transcription	Esophagus	oesophagus
9	chr14:39584200-39588000	Weak transcription	Ovary	ovary
10	chr14:39584200-39592000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr14:39584200-39610800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:39584200-39636000	Weak transcription	Small Intestine	intestine
13	chr14:39584200-39638600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr14:39584400-39587000	Weak transcription	NHDF-Ad	bronchial
15	chr14:39584400-39587200	Weak transcription	Placenta	Placenta
16	chr14:39584400-39587200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr14:39584400-39587400	Weak transcription	Brain Anterior Caudate	brain
18	chr14:39584400-39587400	Weak transcription	NH-A	brain
19	chr14:39584400-39587600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:39584400-39587600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr14:39584400-39588000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr14:39584400-39588200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr14:39584400-39588200	Weak transcription	HSMMtube	muscle
24	chr14:39584400-39591400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr14:39584400-39591800	Weak transcription	Right Ventricle	heart
26	chr14:39584400-39592000	Weak transcription	Brain Substantia Nigra	brain
27	chr14:39584400-39592000	Weak transcription	Fetal Kidney	kidney
28	chr14:39584400-39593400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr14:39584400-39617200	Weak transcription	Psoas Muscle	Psoas
30	chr14:39584400-39620800	Weak transcription	Colonic Mucosa	Colon
31	chr14:39584400-39626600	Weak transcription	Aorta	Aorta
32	chr14:39584600-39586800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr14:39584600-39586800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr14:39584600-39586800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr14:39584600-39586800	Weak transcription	Fetal Thymus	thymus
36	chr14:39584600-39587000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr14:39584600-39587000	Weak transcription	Osteobl	bone
38	chr14:39584600-39587200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr14:39584600-39587200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr14:39584600-39587200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr14:39584600-39587200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr14:39584600-39587200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr14:39584600-39587200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr14:39584600-39587200	Weak transcription	Fetal Intestine Large	intestine
45	chr14:39584600-39587200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr14:39584600-39587200	Weak transcription	NHEK	skin
47	chr14:39584600-39587400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr14:39584600-39587400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr14:39584600-39587400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr14:39584600-39587400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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