Variant report

Variant	rs9312899
Chromosome Location	chr5:1595616-1595617
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1521816..1527528-chr5:1592860..1598605,11	MCF-7	breast:
2	chr5:1514406..1516208-chr5:1594947..1596689,2	MCF-7	breast:
3	chr5:1523398..1525514-chr5:1593049..1596124,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153395	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10043201	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10062417	0.85[ASN][1000 genomes]
rs10064943	0.83[ASN][1000 genomes]
rs1048186	0.85[ASN][1000 genomes]
rs11955318	0.94[ASN][1000 genomes]
rs11958585	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6862954	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6897545	0.83[ASN][1000 genomes]
rs7710273	0.85[ASN][1000 genomes]
rs7734433	0.98[ASN][1000 genomes]
rs7734561	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885250	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880471	chr5:1466813-1598468	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
5	nsv881644	chr5:1478021-1597272	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
6	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
7	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
8	nsv596879	chr5:1519079-1624351	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv881574	chr5:1537141-1598468	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv10657	chr5:1544428-1633373	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv881282	chr5:1549771-1597272	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv596885	chr5:1552255-1624351	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs9312899	CTD-2012J19.1	cis	Artery Tibial	GTEx
rs9312899	CTD-2012J19.1	cis	Skin Sun Exposed Lower leg	GTEx
rs9312899	RP11-43F13.1	cis	Adipose Subcutaneous	GTEx
rs9312899	LOC728613	Cis_1M	lymphoblastoid	RTeQTL
rs9312899	RP11-43F13.1	cis	Whole Blood	GTEx
rs9312899	CTD-2012J19.1	cis	Thyroid	GTEx
rs9312899	RP11-43F13.1	cis	Artery Tibial	GTEx
rs9312899	CTD-2012J19.3	cis	Skin Sun Exposed Lower leg	GTEx
rs9312899	CTD-2012J19.1	cis	Adipose Subcutaneous	GTEx
rs9312899	CTD-2012J19.1	cis	Nerve Tibial	GTEx
rs9312899	RP11-43F13.1	cis	Heart Left Ventricle	GTEx
rs9312899	RP11-43F13.1	cis	Esophagus Muscularis	GTEx
rs9312899	RP11-43F13.1	cis	Muscle Skeletal	GTEx
rs9312899	CTD-2012J19.1	cis	Stomach	GTEx
rs9312899	RP11-43F13.1	cis	Artery Aorta	GTEx
rs9312899	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs9312899	RP11-43F13.1	cis	lung	GTEx
rs9312899	CTD-2012J19.1	cis	Muscle Skeletal	GTEx
rs9312899	RP11-43F13.1	cis	Skin Sun Exposed Lower leg	GTEx
rs9312899	CTD-2012J19.1	cis	lung	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1595000-1595800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:1595000-1596600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:1595000-1597000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:1595000-1597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:1595000-1597200	Weak transcription	Brain Substantia Nigra	brain
6	chr5:1595000-1626600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:1595000-1634000	Weak transcription	Stomach Mucosa	stomach
8	chr5:1595200-1597000	Weak transcription	Fetal Intestine Large	intestine
9	chr5:1595200-1597200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:1595200-1597200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:1595200-1597200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:1595200-1597200	Weak transcription	Adipose Nuclei	Adipose
13	chr5:1595200-1597200	Weak transcription	Brain Anterior Caudate	brain
14	chr5:1595200-1597200	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:1595200-1597200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:1595200-1597200	Weak transcription	Ovary	ovary
17	chr5:1595200-1597200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:1595200-1597200	Weak transcription	HSMM	muscle
19	chr5:1595200-1597200	Weak transcription	HUVEC	blood vessel
20	chr5:1595200-1597200	Weak transcription	K562	blood
21	chr5:1595200-1597200	Weak transcription	NHEK	skin
22	chr5:1595200-1598800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:1595200-1608200	Weak transcription	Primary T cells from cord blood	blood
24	chr5:1595200-1610600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr5:1595200-1610600	Weak transcription	Aorta	Aorta
26	chr5:1595200-1610800	Weak transcription	Fetal Intestine Small	intestine
27	chr5:1595200-1610800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:1595200-1618400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:1595200-1618400	Weak transcription	Liver	Liver
30	chr5:1595200-1618400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:1595200-1618600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:1595200-1632800	Weak transcription	Brain Angular Gyrus	brain
33	chr5:1595200-1632800	Weak transcription	Right Ventricle	heart
34	chr5:1595400-1595800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:1595400-1595800	Enhancers	HepG2	liver
36	chr5:1595400-1597000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr5:1595400-1597000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr5:1595400-1597000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:1595400-1597000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:1595400-1597000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:1595400-1597000	Weak transcription	A549	lung
42	chr5:1595400-1597200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:1595400-1597200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:1595400-1597200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:1595400-1597200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:1595400-1597200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr5:1595400-1597200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:1595400-1597200	Weak transcription	Brain Germinal Matrix	brain
49	chr5:1595400-1597200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr5:1595400-1597200	Weak transcription	Fetal Brain Female	brain

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