Variant report

Variant	rs7734329
Chromosome Location	chr5:179484838-179484839
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	chr5:179483872..179486449-chr5:179497148..179499181,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10051694	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056316	0.88[ASN][1000 genomes]
rs10056991	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059400	0.96[ASN][1000 genomes]
rs10066845	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10071652	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10079029	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10464058	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10464097	0.86[AFR][1000 genomes]
rs11249663	0.81[EUR][1000 genomes]
rs11249664	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11249665	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11249666	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739706	0.81[EUR][1000 genomes]
rs11739898	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11750102	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13162328	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs13435998	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17681274	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2083967	0.81[ASN][1000 genomes]
rs2278662	0.86[JPT][hapmap]
rs34585953	0.84[ASN][1000 genomes]
rs3776946	0.81[EUR][1000 genomes]
rs3776948	0.81[EUR][1000 genomes]
rs4235505	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4264913	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4340879	0.96[YRI][hapmap]
rs4700852	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700854	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700858	1.00[ASW][hapmap];0.96[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs4700859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700862	0.84[ASW][hapmap]
rs4700864	0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs57008562	0.81[EUR][1000 genomes]
rs57117216	0.81[EUR][1000 genomes]
rs62404970	0.81[EUR][1000 genomes]
rs62404974	0.81[EUR][1000 genomes]
rs62404976	0.81[EUR][1000 genomes]
rs62404977	0.81[EUR][1000 genomes]
rs62404979	0.81[EUR][1000 genomes]
rs62405015	0.81[EUR][1000 genomes]
rs6601077	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs6601078	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6861194	0.81[ASN][1000 genomes]
rs6862105	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6869349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6873317	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6873639	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6884565	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6898203	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs7706570	1.00[ASW][hapmap];0.96[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9329095	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9329096	0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7734329	RAB24	cis	parietal	SCAN
rs7734329	RASGEF1C	cis	parietal	SCAN
rs7734329	RNF130	cis	parietal	SCAN
rs7734329	RASGEF1C	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179473800-179488000	Weak transcription	Fetal Stomach	stomach
3	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
4	chr5:179476000-179497800	Weak transcription	Lung	lung
5	chr5:179476400-179486200	Weak transcription	Ovary	ovary
6	chr5:179476400-179487000	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:179476400-179496800	Weak transcription	Right Ventricle	heart
8	chr5:179477400-179494000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:179477400-179495000	Weak transcription	Gastric	stomach
10	chr5:179477600-179486200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:179478000-179496800	Weak transcription	Right Atrium	heart
12	chr5:179478800-179493800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr5:179479800-179496800	Weak transcription	Psoas Muscle	Psoas
14	chr5:179480000-179485400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr5:179480200-179486000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:179480200-179486800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:179480400-179488200	Weak transcription	Fetal Brain Male	brain
18	chr5:179480600-179494000	Weak transcription	Fetal Lung	lung
19	chr5:179480600-179496400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:179481200-179496600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:179481600-179485200	Weak transcription	Fetal Brain Female	brain
22	chr5:179481600-179494600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:179482000-179490200	Weak transcription	HepG2	liver
24	chr5:179482600-179496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:179483400-179485200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr5:179483400-179485200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:179483400-179485400	Enhancers	H9 Cell Line	embryonic stem cell
28	chr5:179483400-179485400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr5:179483800-179486600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:179484000-179485000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:179484000-179485000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:179484000-179486000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr5:179484000-179486000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:179484000-179486000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr5:179484000-179486200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:179484000-179486400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:179484000-179486600	Weak transcription	Brain Angular Gyrus	brain
38	chr5:179484000-179486800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:179484200-179485000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:179484200-179486000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:179484200-179486000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:179484200-179486000	Weak transcription	Brain Substantia Nigra	brain
43	chr5:179484200-179486600	Weak transcription	Brain Hippocampus Middle	brain
44	chr5:179484200-179486800	Weak transcription	Brain Anterior Caudate	brain
45	chr5:179484200-179488200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:179484200-179488200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:179484200-179489800	Weak transcription	NHEK	skin
48	chr5:179484200-179496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:179484400-179485000	Weak transcription	Aorta	Aorta
50	chr5:179484400-179486800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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