Variant report

Variant	rs10056991
Chromosome Location	chr5:179485315-179485316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179484896..179487600-chr5:179495650..179498856,3	K562	blood:
2	chr5:179483872..179486449-chr5:179497148..179499181,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10051632	0.87[AFR][1000 genomes]
rs10051694	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056316	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10059400	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10066845	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10071652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10079029	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10464058	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11249663	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11249664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11249665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11249666	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739706	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11739898	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap]
rs11748441	0.90[EUR][1000 genomes]
rs11750102	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13435998	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17681274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2083967	0.81[ASN][1000 genomes]
rs2278662	0.86[JPT][hapmap]
rs34585953	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3776946	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3776948	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4235505	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4264913	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700854	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700859	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700864	0.83[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs57008562	0.92[EUR][1000 genomes]
rs57117216	0.92[EUR][1000 genomes]
rs61356660	0.90[EUR][1000 genomes]
rs62404970	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62404974	0.93[EUR][1000 genomes]
rs62404976	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62404977	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62404979	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62405015	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6601077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6601078	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6861194	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6862105	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6869349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6873317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6873639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6884565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6898203	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs7729516	0.93[EUR][1000 genomes]
rs7734329	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]
rs9329095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10056991	GRM6	cis	cerebellum	SCAN
rs10056991	TRIM7	cis	parietal	SCAN
rs10056991	RASGEF1C	cis	parietal	SCAN
rs10056991	PROP1	cis	parietal	SCAN
rs10056991	RASGEF1C	cis	cerebellum	SCAN
rs10056991	LTC4S	cis	cerebellum	SCAN
rs10056991	CLTB	cis	parietal	SCAN
rs10056991	C5orf45	cis	parietal	SCAN

Chromatin state (count:62 , 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	chr5:179481600-179494600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:179482000-179490200	Weak transcription	HepG2	liver
23	chr5:179482600-179496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:179483400-179485400	Enhancers	H9 Cell Line	embryonic stem cell
25	chr5:179483400-179485400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr5:179483800-179486600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:179484000-179486000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:179484000-179486000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:179484000-179486000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:179484000-179486200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:179484000-179486400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:179484000-179486600	Weak transcription	Brain Angular Gyrus	brain
33	chr5:179484000-179486800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:179484200-179486000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:179484200-179486000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:179484200-179486000	Weak transcription	Brain Substantia Nigra	brain
37	chr5:179484200-179486600	Weak transcription	Brain Hippocampus Middle	brain
38	chr5:179484200-179486800	Weak transcription	Brain Anterior Caudate	brain
39	chr5:179484200-179488200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:179484200-179488200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:179484200-179489800	Weak transcription	NHEK	skin
42	chr5:179484200-179496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:179484400-179486800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:179484400-179486800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:179484400-179487200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr5:179484400-179490000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:179484400-179495000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:179484600-179485400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr5:179484600-179485400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:179484600-179486200	Strong transcription	Monocytes-CD14+_RO01746	blood

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