Variant report

Variant	rs10479515
Chromosome Location	chr5:178296074-178296075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178285911..178288443-chr5:178294689..178296630,2	K562	blood:
2	chr5:178286202..178288333-chr5:178295235..178296864,2	MCF-7	breast:
3	chr5:178290096..178292803-chr5:178294356..178296794,2	K562	blood:

Variant related genes	Relation type
ENSG00000178338	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10035887	0.88[EUR][1000 genomes]
rs10040956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077950	0.83[CHB][hapmap]
rs1046726	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10479516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516151	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs11249603	0.85[EUR][1000 genomes]
rs11743869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746382	0.84[EUR][1000 genomes]
rs11955586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960446	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655480	0.83[CHB][hapmap]
rs12658098	0.83[CHB][hapmap]
rs13154558	0.87[EUR][1000 genomes]
rs1496949	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1496950	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs17078820	0.81[JPT][hapmap]
rs17078829	0.81[JPT][hapmap]
rs1995079	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs4130052	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700927	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs62393052	0.89[EUR][1000 genomes]
rs6600990	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6866021	0.88[EUR][1000 genomes]
rs6870709	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872605	0.87[EUR][1000 genomes]
rs6872794	0.87[EUR][1000 genomes]
rs6873993	0.87[EUR][1000 genomes]
rs6877198	0.84[CHB][hapmap]
rs6885597	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891035	0.84[CHB][hapmap]
rs7445694	0.83[CHB][hapmap]
rs7446225	0.83[CHB][hapmap]
rs7447547	0.83[CHB][hapmap]
rs7701607	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs7702579	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7702879	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs9329059	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv462574	chr5:178269682-178313078	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv600463	chr5:178269682-178313078	Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv823352	chr5:178279625-178296623	Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178287600-178296200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:178287600-178302400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr5:178288400-178299200	Strong transcription	Fetal Muscle Trunk	muscle
5	chr5:178288600-178299400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:178288800-178297600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:178288800-178300000	Strong transcription	Fetal Lung	lung
8	chr5:178288800-178302200	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:178289000-178297000	Strong transcription	Fetal Stomach	stomach
11	chr5:178289000-178297400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:178289000-178297400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr5:178289000-178299600	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:178289000-178301000	Strong transcription	Fetal Muscle Leg	muscle
15	chr5:178289000-178301600	Weak transcription	Stomach Mucosa	stomach
16	chr5:178289200-178299000	Strong transcription	Fetal Brain Female	brain
17	chr5:178289400-178302200	Strong transcription	Brain Anterior Caudate	brain
18	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:178289800-178297200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:178289800-178297600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:178289800-178299000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:178289800-178300200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:178289800-178300200	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr5:178290000-178299400	Weak transcription	Fetal Heart	heart
25	chr5:178290000-178302200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:178290200-178297800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr5:178290600-178298600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:178290600-178298600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:178290600-178299000	Weak transcription	Fetal Brain Male	brain
30	chr5:178290600-178299600	Strong transcription	Brain Germinal Matrix	brain
31	chr5:178290600-178299800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:178290600-178301200	Strong transcription	Brain Cingulate Gyrus	brain
33	chr5:178290800-178298800	Strong transcription	Primary T cells from cord blood	blood
34	chr5:178290800-178300200	Strong transcription	Left Ventricle	heart
35	chr5:178291000-178298400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:178291000-178299200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:178291000-178299200	Strong transcription	Fetal Thymus	thymus
38	chr5:178291000-178300000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:178291200-178317400	ZNF genes & repeats	Liver	Liver
40	chr5:178291400-178298000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr5:178291400-178300200	Strong transcription	Dnd41	blood
42	chr5:178291600-178299000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:178291800-178299000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
44	chr5:178292000-178303000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr5:178292200-178299200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:178292200-178302200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:178292400-178296400	Strong transcription	Pancreatic Islets	Pancreatic Islet
48	chr5:178292400-178297400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr5:178292600-178296200	Strong transcription	Adipose Nuclei	Adipose
50	chr5:178292600-178298600	Strong transcription	Brain Hippocampus Middle	brain

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