Variant report

Variant	rs5745568
Chromosome Location	chr6:33548394-33548395
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT5A	chr6:33547946-33548415	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:33547758-33548418	H1-neurons	neurons:	n/a	n/a
3	MAZ	chr6:33547858-33548484	IMR90	lung:	n/a	n/a
4	MAFK	chr6:33547864-33548450	Hela-S3	cervix:	n/a	n/a
5	MTA3	chr6:33547740-33548408	GM12878	blood:	n/a	n/a
6	GABPA	chr6:33547261-33548463	MCF-7	breast:	n/a	n/a
7	ARID3A	chr6:33547880-33548462	HepG2	liver:	n/a	n/a
8	SP1	chr6:33547797-33548401	H1-hESC	embryonic stem cell:	n/a	chr6:33548135-33548146 chr6:33548122-33548133
9	ZC3H11A	chr6:33547995-33548402	K562	blood:	n/a	n/a
10	MYBL2	chr6:33547341-33548454	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:33547618-33548436	HUVEC	blood vessel:	n/a	n/a
12	JUN	chr6:33547534-33548483	K562	blood:	n/a	n/a
13	MYBL2	chr6:33547794-33548523	HepG2	liver:	n/a	n/a
14	MAX	chr6:33547937-33548411	ECC-1	luminal epithelium:	n/a	n/a
15	NR2F2	chr6:33547114-33548401	K562	blood:	n/a	n/a
16	TCF7L2	chr6:33548089-33548406	HEK293	kidney:	n/a	chr6:33548210-33548226 chr6:33548214-33548223 chr6:33548210-33548226 chr6:33548211-33548225
17	CREB1	chr6:33547424-33548490	HepG2	liver:	n/a	n/a
18	CBX3	chr6:33547799-33548432	K562	blood:	n/a	n/a
19	GABPA	chr6:33547753-33548396	SK-N-SH	brain:	n/a	n/a
20	FOXA1	chr6:33548171-33548454	HepG2	liver:	n/a	n/a
21	CREB1	chr6:33547924-33548495	HepG2	liver:	n/a	n/a
22	CUX1	chr6:33547967-33548394	K562	blood:	n/a	n/a
23	POLR2A	chr6:33547632-33548506	SK-N-MC	brain:	n/a	n/a
24	FOXA2	chr6:33548081-33548559	A549	lung:	n/a	n/a
25	POLR2A	chr6:33547906-33548435	H1-neurons	neurons:	n/a	n/a
26	SIN3A	chr6:33547488-33548417	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:33547714-33548403	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr6:33547659-33548409	PFSK-1	brain:	n/a	n/a
29	MXI1	chr6:33547359-33548617	SK-N-SH	brain:	n/a	n/a
30	GABPA	chr6:33547476-33548404	K562	blood:	n/a	n/a
31	POLR2A	chr6:33547445-33548501	PFSK-1	brain:	n/a	n/a
32	MAX	chr6:33547762-33548507	A549	lung:	n/a	n/a
33	FOXA2	chr6:33548203-33548417	HepG2	liver:	n/a	n/a
34	FOXA1	chr6:33548205-33548444	T-47D	breast:	n/a	n/a
35	GABPA	chr6:33547797-33548455	HL-60	blood:	n/a	n/a
36	HCFC1	chr6:33547752-33548480	Hela-S3	cervix:	n/a	n/a
37	KAP1	chr6:33548007-33548417	U2OS	brain:	n/a	n/a
38	REST	chr6:33547519-33548654	H1-neurons	neurons:	n/a	chr6:33548107-33548120
39	NFIC	chr6:33547995-33548469	HepG2	liver:	n/a	n/a
40	FOXA1	chr6:33548046-33548484	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33381203..33384118-chr6:33546265..33549089,2	K562	blood:
2	chr19:50432772..50433317-chr6:33548039..33548579,2	NB4	blood:
3	chr6:33538758..33539282-chr6:33548033..33548541,2	K562	blood:
4	chr6:33394086..33395846-chr6:33548309..33550543,2	K562	blood:
5	chr6:33546298..33549471-chr6:33550091..33553469,5	K562	blood:
6	chr6:33546546..33549178-chr6:33588334..33590241,2	K562	blood:

No data

Variant related genes	Relation type
GGNBP1	TF binding region
BAK1	TF binding region
ENSG00000112511	Chromatin interaction
ENSG00000204188	Chromatin interaction
ENSG00000104951	Chromatin interaction
ENSG00000213024	Chromatin interaction
ENSG00000096433	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10807126	0.86[ASN][1000 genomes]
rs10947409	0.86[ASN][1000 genomes]
rs11968218	0.86[ASN][1000 genomes]
rs12206050	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12213869	0.87[GIH][hapmap]
rs12214883	0.85[ASN][1000 genomes]
rs3748079	0.86[GIH][hapmap]
rs3846855	0.94[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs510153	0.87[GIH][hapmap]
rs5745582	0.93[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5745587	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914422	0.90[ASN][1000 genomes]
rs9296095	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357161	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366824	0.86[ASN][1000 genomes]
rs9380365	0.88[CHB][hapmap]
rs9380371	0.90[ASN][1000 genomes]
rs9469485	1.00[CHB][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Platelet counts	20139978	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5745568	CDKN1A	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33546000-33548400	Flanking Active TSS	Primary B cells from peripheral blood	blood
2	chr6:33546800-33548400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:33546800-33548400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:33546800-33548400	Active TSS	Left Ventricle	heart
5	chr6:33547000-33548400	Active TSS	Fetal Kidney	kidney
6	chr6:33547000-33548400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr6:33547200-33548400	Flanking Active TSS	Fetal Muscle Trunk	muscle
8	chr6:33547400-33548400	Active TSS	Fetal Brain Female	brain
9	chr6:33547400-33548400	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr6:33547400-33548400	Active TSS	Right Atrium	heart
11	chr6:33547600-33548400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:33547600-33548400	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr6:33547600-33548400	Active TSS	Colonic Mucosa	Colon
14	chr6:33547800-33548400	Active TSS	Right Ventricle	heart
15	chr6:33548000-33548400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:33548000-33548400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:33548000-33548400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr6:33548000-33548400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:33548000-33548400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr6:33548000-33548400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:33548000-33548400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:33548000-33548400	Enhancers	Fetal Heart	heart
23	chr6:33548000-33548400	Flanking Active TSS	Fetal Stomach	stomach
24	chr6:33548000-33548400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr6:33548000-33548400	Flanking Active TSS	Dnd41	blood
26	chr6:33548000-33548400	Flanking Active TSS	HMEC	breast
27	chr6:33548000-33548400	Enhancers	HUVEC	blood vessel
28	chr6:33548000-33548600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:33548000-33548600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:33548000-33548600	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr6:33548000-33548800	Enhancers	Stomach Mucosa	stomach
32	chr6:33548200-33548400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr6:33548200-33548400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
34	chr6:33548200-33548400	Enhancers	H9 Cell Line	embryonic stem cell
35	chr6:33548200-33548400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:33548200-33548400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:33548200-33548400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:33548200-33548400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr6:33548200-33548400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:33548200-33548400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr6:33548200-33548400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:33548200-33548400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr6:33548200-33548400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr6:33548200-33548400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr6:33548200-33548400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:33548200-33548400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:33548200-33548400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:33548200-33548400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:33548200-33548400	Enhancers	Primary B cells from cord blood	blood
50	chr6:33548200-33548400	Enhancers	Primary hematopoietic stem cells	blood

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