Variant report

Variant	rs17647689
Chromosome Location	chr5:15683413-15683414
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	chr5:15683076..15684017-chr5:15995401..15996222,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10434653	0.91[ASN][1000 genomes]
rs10434654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10520823	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1127792	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12515169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12516275	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs12517648	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs12518052	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12519070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12520066	0.98[ASN][1000 genomes]
rs12522526	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs12522561	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs12655750	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1505040	1.00[YRI][hapmap]
rs16867546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16867549	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs16867589	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs17647713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17647886	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs17647898	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs17704227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17704245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1864220	0.82[JPT][hapmap]
rs4296803	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs4377704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4391162	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs4593267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4701643	1.00[JPT][hapmap]
rs58200321	0.85[ASN][1000 genomes]
rs58908332	0.89[ASN][1000 genomes]
rs73752499	0.89[ASN][1000 genomes]
rs73755514	0.83[ASN][1000 genomes]
rs73755515	0.87[ASN][1000 genomes]
rs73755516	0.87[ASN][1000 genomes]
rs73755517	0.87[ASN][1000 genomes]
rs9637832	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9790923	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1028089	chr5:15636285-15883910	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv537676	chr5:15636285-15883910	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1024248	chr5:15638067-15863583	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv537677	chr5:15638067-15863583	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv880755	chr5:15670377-15938553	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv597263	chr5:15672137-15720478	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv461983	chr5:15674635-15720106	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv597264	chr5:15674635-15720106	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv2757107	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv2759327	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15672200-15684400	Weak transcription	NHDF-Ad	bronchial
2	chr5:15674400-15684200	Weak transcription	HSMMtube	muscle
3	chr5:15675200-15687000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:15675200-15693000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:15675800-15686200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:15676000-15686000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:15676000-15687200	Weak transcription	Brain Angular Gyrus	brain
8	chr5:15677000-15690800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:15678600-15684600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:15679600-15684400	Weak transcription	HSMM	muscle
11	chr5:15680000-15687000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:15681000-15686400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:15681000-15687000	Weak transcription	Right Ventricle	heart
14	chr5:15681200-15684400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:15681400-15684400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:15682000-15687200	Enhancers	Fetal Heart	heart
17	chr5:15682200-15683600	Enhancers	Left Ventricle	heart
18	chr5:15682200-15683600	Enhancers	Right Atrium	heart
19	chr5:15682400-15690800	Weak transcription	Aorta	Aorta
20	chr5:15682800-15683800	Enhancers	Colon Smooth Muscle	Colon
21	chr5:15682800-15684600	Enhancers	Fetal Kidney	kidney
22	chr5:15682800-15684600	Enhancers	Fetal Stomach	stomach
23	chr5:15683000-15683600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr5:15683000-15683600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr5:15683000-15683800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:15683200-15683600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:15683200-15683800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:15683200-15684000	Enhancers	Adipose Nuclei	Adipose
29	chr5:15683200-15684000	Enhancers	Fetal Lung	lung
30	chr5:15683200-15684000	Enhancers	HUVEC	blood vessel
31	chr5:15683400-15683600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:15683400-15683800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:15683400-15683800	Enhancers	Ovary	ovary
34	chr5:15683400-15684400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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