Variant report

Variant	rs10059629
Chromosome Location	chr5:90169163-90169164
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:90168826..90171569-chr5:90675528..90678238,2	MCF-7	breast:
2	chr5:90167555..90169538-chr5:90678954..90680589,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10044202	0.83[ASN][1000 genomes]
rs10045071	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10052015	0.92[CHB][hapmap]
rs10053303	0.89[CEU][hapmap];0.92[CHB][hapmap]
rs10060641	0.92[CHB][hapmap]
rs10061193	0.84[ASN][1000 genomes]
rs10078496	0.92[CHB][hapmap]
rs10474336	0.83[CHB][hapmap]
rs10514340	0.89[CEU][hapmap]
rs12054681	0.92[CHB][hapmap]
rs12520956	0.91[CHB][hapmap]
rs12522395	0.84[CHB][hapmap]
rs13159353	0.89[ASN][1000 genomes]
rs16869175	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16869247	0.82[CEU][hapmap]
rs2247415	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2366935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438338	0.92[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2438342	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2438343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2438344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2438345	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2438351	0.83[CHB][hapmap]
rs2438353	1.00[CHB][hapmap]
rs2443068	0.92[CHB][hapmap];0.93[YRI][hapmap];0.96[ASN][1000 genomes]
rs28437109	0.81[ASN][1000 genomes]
rs3098356	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4916698	0.88[CEU][hapmap];0.92[CHB][hapmap]
rs4916826	0.84[ASN][1000 genomes]
rs4916827	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs4916828	0.83[ASN][1000 genomes]
rs4916829	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs57107124	0.87[ASN][1000 genomes]
rs6865577	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6878896	0.92[CHB][hapmap]
rs7724016	0.92[CHB][hapmap]
rs881289	0.89[CHB][hapmap]

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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90112000-90175800	Weak transcription	Fetal Brain Female	brain
2	chr5:90148200-90171400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:90151800-90174000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:90151800-90174600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:90163600-90171200	Weak transcription	Fetal Kidney	kidney
6	chr5:90163600-90194400	Weak transcription	Pancreas	Pancrea
7	chr5:90164400-90174400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:90164400-90174800	Enhancers	Liver	Liver
9	chr5:90165400-90188800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:90166000-90171200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:90166200-90171200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:90166200-90171200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:90166200-90171800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:90166400-90170000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:90166400-90171200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:90166400-90174000	Weak transcription	K562	blood
17	chr5:90166600-90174600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:90167400-90169200	Enhancers	Fetal Lung	lung
19	chr5:90167400-90169200	Enhancers	Stomach Mucosa	stomach
20	chr5:90167400-90170400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr5:90167600-90170200	Enhancers	Ovary	ovary
22	chr5:90167600-90171600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:90167800-90173200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:90168200-90169200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr5:90168200-90186000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:90168400-90169200	Enhancers	Primary hematopoietic stem cells	blood
27	chr5:90168400-90169200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr5:90168400-90169200	Enhancers	Colon Smooth Muscle	Colon
29	chr5:90168400-90169200	Enhancers	HepG2	liver
30	chr5:90168400-90169400	Enhancers	Aorta	Aorta
31	chr5:90168400-90169600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:90168400-90170200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr5:90168400-90170400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr5:90168600-90169400	Enhancers	A549	lung
35	chr5:90168800-90169200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr5:90168800-90169200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:90168800-90169200	Enhancers	Duodenum Mucosa	Duodenum
38	chr5:90168800-90169200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr5:90168800-90169600	Enhancers	Psoas Muscle	Psoas
40	chr5:90168800-90169800	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr5:90168800-90170000	Enhancers	Fetal Thymus	thymus
42	chr5:90168800-90170400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr5:90168800-90170400	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr5:90169000-90170400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr5:90169000-90174200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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