Variant report

Variant	rs17616038
Chromosome Location	chr14:39504579-39504580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39190911..39191748-chr14:39503600..39504605,4	MCF-7	breast:
2	chr14:39074185..39074840-chr14:39504069..39505004,2	MCF-7	breast:
3	chr14:39504261..39505866-chr14:39507926..39509842,2	K562	blood:

Variant related genes	Relation type
ENSG00000271468	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10459481	0.90[YRI][hapmap]
rs10872914	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10872915	0.92[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs11157039	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11157040	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11558739	0.85[CEU][hapmap];0.96[YRI][hapmap]
rs11620885	0.89[AFR][1000 genomes]
rs11628065	0.92[CEU][hapmap]
rs12184985	0.89[AFR][1000 genomes]
rs12432236	0.92[CEU][hapmap]
rs12435383	0.90[CEU][hapmap]
rs12436766	0.85[CEU][hapmap];0.95[YRI][hapmap]
rs17108710	0.93[ASN][1000 genomes]
rs17108729	0.93[ASN][1000 genomes]
rs17108735	0.93[ASN][1000 genomes]
rs17108737	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17616116	0.86[CEU][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17678780	0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs1884385	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038358	0.84[ASN][1000 genomes]
rs2273316	1.00[CEU][hapmap]
rs2415523	0.93[ASN][1000 genomes]
rs4902326	0.84[ASN][1000 genomes]
rs56869057	0.93[ASN][1000 genomes]
rs57014289	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57049071	0.92[AFR][1000 genomes]
rs57120608	0.85[AFR][1000 genomes]
rs58589656	0.90[ASN][1000 genomes]
rs60444423	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62001129	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7157388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8005437	0.93[ASN][1000 genomes]
rs8007642	0.90[ASN][1000 genomes]
rs9322995	0.85[CEU][hapmap];0.95[YRI][hapmap]
rs970622	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9788627	0.85[CEU][hapmap];0.95[YRI][hapmap]

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	chr14:39487200-39508600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr14:39493400-39505800	Weak transcription	Psoas Muscle	Psoas
3	chr14:39495400-39505000	Weak transcription	Small Intestine	intestine
4	chr14:39495400-39505800	Weak transcription	Fetal Kidney	kidney
5	chr14:39495400-39518200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr14:39495600-39509800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:39495800-39516000	Weak transcription	Stomach Mucosa	stomach
8	chr14:39496000-39514800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:39496000-39520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr14:39496600-39507800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:39497400-39506000	Weak transcription	Fetal Heart	heart
12	chr14:39497400-39518000	Strong transcription	HSMM	muscle
13	chr14:39497400-39519200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr14:39497600-39507600	Weak transcription	Brain Germinal Matrix	brain
15	chr14:39497800-39505800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr14:39497800-39520400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr14:39497800-39521200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr14:39498000-39505800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr14:39498000-39510000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr14:39498000-39518400	Strong transcription	Osteobl	bone
21	chr14:39498000-39518600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr14:39498000-39524200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr14:39498200-39507600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr14:39498200-39509400	Weak transcription	Fetal Brain Male	brain
25	chr14:39498200-39510200	Strong transcription	Placenta	Placenta
26	chr14:39498200-39519400	Strong transcription	NH-A	brain
27	chr14:39498200-39524200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr14:39498200-39524400	Strong transcription	Fetal Intestine Large	intestine
29	chr14:39498400-39520000	Strong transcription	HepG2	liver
30	chr14:39498400-39524800	Weak transcription	K562	blood
31	chr14:39498600-39510000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr14:39498600-39518000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr14:39498600-39519600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr14:39498600-39524000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr14:39498600-39524800	Strong transcription	Adipose Nuclei	Adipose
36	chr14:39499000-39507800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr14:39499000-39510200	Strong transcription	NHDF-Ad	bronchial
38	chr14:39499000-39510400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr14:39499000-39510400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr14:39499000-39510400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr14:39499000-39523200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr14:39499000-39523600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr14:39499000-39524200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr14:39499000-39524800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr14:39499000-39524800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr14:39499000-39525000	Strong transcription	Liver	Liver
47	chr14:39499600-39524600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr14:39499800-39509000	Weak transcription	Brain Substantia Nigra	brain
49	chr14:39500000-39504800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr14:39500000-39505600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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