Variant report

Variant	rs72677559
Chromosome Location	chr1:46603363-46603364
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46602958-46603486	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46602297..46604849-chr1:46618542..46621486,2	K562	blood:
2	chr1:46601377..46603890-chr1:46611538..46613763,2	MCF-7	breast:
3	chr1:46603018..46605459-chr1:46613609..46615653,2	MCF-7	breast:
4	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
5	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:

No data

Variant related genes	Relation type
PIK3R3	TF binding region
ENSG00000117461	Chromatin interaction
ENSG00000250719	Chromatin interaction
ENSG00000117472	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10749861	1.00[ASN][1000 genomes]
rs10789482	1.00[ASN][1000 genomes]
rs11211247	1.00[ASN][1000 genomes]
rs11580953	1.00[ASN][1000 genomes]
rs11584814	1.00[ASN][1000 genomes]
rs11587648	1.00[ASN][1000 genomes]
rs11805376	1.00[ASN][1000 genomes]
rs12045409	1.00[ASN][1000 genomes]
rs12047120	1.00[ASN][1000 genomes]
rs1355641	1.00[ASN][1000 genomes]
rs17855317	1.00[ASN][1000 genomes]
rs2067635	1.00[ASN][1000 genomes]
rs3795318	1.00[ASN][1000 genomes]
rs4256763	1.00[ASN][1000 genomes]
rs4300171	1.00[ASN][1000 genomes]
rs4364819	1.00[ASN][1000 genomes]
rs4382655	1.00[ASN][1000 genomes]
rs4388641	1.00[ASN][1000 genomes]
rs4660330	1.00[ASN][1000 genomes]
rs4660333	1.00[ASN][1000 genomes]
rs4660901	1.00[ASN][1000 genomes]
rs4660909	1.00[ASN][1000 genomes]
rs55641506	1.00[ASN][1000 genomes]
rs55652826	1.00[ASN][1000 genomes]
rs55735913	1.00[ASN][1000 genomes]
rs55765474	1.00[ASN][1000 genomes]
rs56047133	1.00[ASN][1000 genomes]
rs56140667	1.00[ASN][1000 genomes]
rs56278140	1.00[ASN][1000 genomes]
rs56295206	1.00[ASN][1000 genomes]
rs56301932	1.00[ASN][1000 genomes]
rs56368769	1.00[ASN][1000 genomes]
rs6429590	1.00[ASN][1000 genomes]
rs6429592	1.00[ASN][1000 genomes]
rs6429593	1.00[ASN][1000 genomes]
rs6669534	1.00[ASN][1000 genomes]
rs6685465	1.00[ASN][1000 genomes]
rs6689417	1.00[ASN][1000 genomes]
rs6693222	1.00[ASN][1000 genomes]
rs6696284	1.00[ASN][1000 genomes]
rs6700322	1.00[ASN][1000 genomes]
rs6700974	1.00[ASN][1000 genomes]
rs72677518	1.00[ASN][1000 genomes]
rs72677530	1.00[ASN][1000 genomes]
rs72677533	1.00[ASN][1000 genomes]
rs72677541	1.00[ASN][1000 genomes]
rs72677543	1.00[ASN][1000 genomes]
rs72677545	1.00[ASN][1000 genomes]
rs72677546	1.00[ASN][1000 genomes]
rs72677550	1.00[ASN][1000 genomes]
rs72677553	1.00[ASN][1000 genomes]
rs72677556	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72677557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72690901	1.00[ASN][1000 genomes]
rs72692603	1.00[ASN][1000 genomes]
rs72692613	1.00[ASN][1000 genomes]
rs72692632	1.00[ASN][1000 genomes]
rs72692639	1.00[ASN][1000 genomes]
rs7530480	1.00[ASN][1000 genomes]
rs7532388	1.00[ASN][1000 genomes]
rs7533750	1.00[ASN][1000 genomes]
rs7548617	1.00[ASN][1000 genomes]
rs7552810	1.00[ASN][1000 genomes]
rs7555458	1.00[ASN][1000 genomes]
rs884443	1.00[ASN][1000 genomes]
rs9429090	1.00[ASN][1000 genomes]
rs9429093	1.00[ASN][1000 genomes]
rs9429179	1.00[ASN][1000 genomes]
rs9429184	1.00[ASN][1000 genomes]
rs9429187	1.00[ASN][1000 genomes]
rs9429188	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs72677559	CCDC163P	cis	Thyroid	GTEx
rs72677559	CCDC163P	cis	Nerve Tibial	GTEx
rs72677559	CCDC163P	cis	Artery Tibial	GTEx
rs72677559	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs72677559	CCDC163P	cis	Heart Left Ventricle	GTEx
rs72677559	CCDC163P	cis	lung	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46599600-46604000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr1:46600000-46604000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:46600600-46603400	Weak transcription	HSMM	muscle
4	chr1:46601000-46603400	Weak transcription	K562	blood
5	chr1:46601000-46603400	Weak transcription	NH-A	brain
6	chr1:46601200-46603400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:46601400-46603400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:46601400-46603600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:46602200-46603800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:46602200-46604000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:46602200-46604000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:46602200-46604000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:46602400-46603400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:46602400-46603600	Enhancers	Left Ventricle	heart
15	chr1:46602400-46603800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:46602400-46604000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:46602400-46604200	Enhancers	Fetal Muscle Leg	muscle
18	chr1:46602600-46603800	Enhancers	Fetal Kidney	kidney
19	chr1:46602600-46604600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:46603000-46604400	Enhancers	Right Atrium	heart
21	chr1:46603200-46603400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:46603200-46603400	Enhancers	Duodenum Mucosa	Duodenum
23	chr1:46603200-46603400	Enhancers	Fetal Intestine Large	intestine
24	chr1:46603200-46603400	Enhancers	Fetal Stomach	stomach
25	chr1:46603200-46603400	Flanking Active TSS	Ovary	ovary
26	chr1:46603200-46603400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:46603200-46603400	Enhancers	HUVEC	blood vessel
28	chr1:46603200-46603400	Active TSS	NHLF	lung
29	chr1:46603200-46603600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:46603200-46603600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:46603200-46603600	Enhancers	Liver	Liver
32	chr1:46603200-46603600	Enhancers	HSMMtube	muscle
33	chr1:46603200-46603800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:46603200-46603800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:46603200-46603800	Enhancers	Adipose Nuclei	Adipose
36	chr1:46603200-46603800	Enhancers	Fetal Lung	lung
37	chr1:46603200-46603800	Flanking Active TSS	Hela-S3	cervix
38	chr1:46603200-46603800	Flanking Active TSS	HepG2	liver
39	chr1:46603200-46604000	Flanking Active TSS	Osteobl	bone
40	chr1:46603200-46604400	Enhancers	Fetal Muscle Trunk	muscle

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