Variant report

Variant	rs7566
Chromosome Location	chr5:179156449-179156450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179156266-179156578	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:179156326-179156566	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:179156276-179156664	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:179156416-179156514	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:179156222-179156649	HL-60	blood:	n/a	n/a
6	POLR2A	chr5:179156251-179156670	K562	blood:	n/a	n/a
7	SP1	chr5:179156177-179156796	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr5:179156257-179156688	K562	blood:	n/a	n/a
9	POLR2A	chr5:179156229-179156640	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr5:179156362-179156574	MCF-7	breast:	n/a	n/a
11	POLR2A	chr5:179156336-179156632	HepG2	liver:	n/a	n/a
12	WRNIP1	chr5:179156347-179156475	GM12878	blood:	n/a	n/a
13	CTCF	chr5:179156400-179156550	HEK293	kidney:	n/a	n/a
14	POLR2A	chr5:179156226-179156592	K562	blood:	n/a	n/a
15	POLR2A	chr5:179156366-179156565	HepG2	liver:	n/a	n/a
16	POLR2A	chr5:179156266-179156573	GM12891	blood:	n/a	n/a
17	POLR2A	chr5:179156244-179156839	HL-60	blood:	n/a	n/a
18	CTCF	chr5:179156274-179156670	T-47D	breast:	n/a	n/a
19	POLR2A	chr5:179153683-179159964	K562	blood:	n/a	n/a
20	POLR2A	chr5:179156248-179156688	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179125428..179127491-chr5:179155880..179157495,2	K562	blood:
2	chr5:179152255..179157364-chr5:179157617..179161141,8	K562	blood:
3	chr5:179122873..179128898-chr5:179155888..179164921,20	K562	blood:
4	chr5:179147273..179149282-chr5:179155008..179157587,2	MCF-7	breast:
5	chr5:179129274..179131035-chr5:179155362..179157938,2	K562	blood:
6	chr5:179143486..179153989-chr5:179156108..179164461,19	MCF-7	breast:
7	chr5:179154467..179157010-chr5:179247378..179249418,2	K562	blood:
8	chr5:179133916..179136013-chr5:179154782..179157168,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAML1-1	chr5:179156361-179156650	NONHSAT105617

No data

Variant related genes	Relation type
MAML1	TF binding region
ENSG00000161021	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000161011	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10516140	1.00[JPT][hapmap]
rs11738962	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11747219	0.81[CEU][hapmap]
rs11747643	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12654954	0.96[ASN][1000 genomes]
rs166624	0.84[JPT][hapmap]
rs2890060	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4441842	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4504352	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4526069	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700839	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4701197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6627	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6877064	0.85[JPT][hapmap]
rs6879613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71613416	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7700649	0.81[CEU][hapmap]
rs7723450	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];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9800237	0.83[AFR][1000 genomes];0.92[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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7566	PRR7	cis	cerebellum	SCAN
rs7566	CANX	cis	parietal	SCAN
rs7566	MAML1	cis	lymphoblastoid	seeQTL
rs7566	HRH2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179127800-179156600	Strong transcription	Fetal Stomach	stomach
2	chr5:179127800-179158200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:179128400-179157800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:179128400-179157800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:179128400-179158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:179128400-179159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:179128600-179158200	Strong transcription	Fetal Muscle Leg	muscle
8	chr5:179129000-179158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:179129200-179157600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr5:179129400-179158200	Strong transcription	Fetal Thymus	thymus
11	chr5:179129600-179157400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:179129800-179158200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:179129800-179158200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:179129800-179158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:179129800-179158200	Strong transcription	Fetal Intestine Large	intestine
16	chr5:179129800-179158800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:179130400-179158200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:179130600-179157000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:179130600-179157600	Strong transcription	HUVEC	blood vessel
20	chr5:179130800-179158200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr5:179130800-179158200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:179130800-179159800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:179131000-179157600	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr5:179131000-179157800	Strong transcription	Dnd41	blood
25	chr5:179131000-179158200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:179131200-179158000	Strong transcription	Placenta	Placenta
27	chr5:179132000-179158200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr5:179132400-179157400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr5:179132400-179157400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr5:179132800-179156600	Strong transcription	Lung	lung
31	chr5:179132800-179158200	Strong transcription	Adipose Nuclei	Adipose
32	chr5:179132800-179158200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr5:179133000-179158000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:179133000-179158200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:179133000-179158200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:179133000-179158200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:179133000-179158200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:179133200-179158400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:179133200-179158600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:179133200-179158800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:179133400-179157000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr5:179133600-179156600	Strong transcription	Thymus	Thymus
43	chr5:179133600-179158200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr5:179133800-179156600	Strong transcription	Colonic Mucosa	Colon
45	chr5:179136600-179156800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr5:179138400-179159000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:179139400-179156600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr5:179139400-179157600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr5:179139400-179157800	Strong transcription	Left Ventricle	heart
50	chr5:179139400-179158000	Strong transcription	H9 Cell Line	embryonic stem cell

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