Variant report

Variant	rs1455869
Chromosome Location	chr3:160475488-160475489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr3:160475391-160475765	H1-hESC	embryonic stem cell:	n/a	chr3:160475637-160475655
2	POLR2A	chr3:160474918-160475701	H1-hESC	embryonic stem cell:	n/a	n/a
3	FOXA1	chr3:160475468-160475951	HepG2	liver:	n/a	n/a
4	E2F6	chr3:160474910-160475732	H1-hESC	embryonic stem cell:	n/a	chr3:160475450-160475459
5	YY1	chr3:160475217-160475779	H1-hESC	embryonic stem cell:	n/a	chr3:160475569-160475580
6	MAX	chr3:160475135-160475877	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr3:160475156-160475648	H1-hESC	embryonic stem cell:	n/a	chr3:160475450-160475459
8	SPI1	chr3:160475375-160475799	HL-60	blood:	n/a	chr3:160475550-160475563
9	TAF1	chr3:160474886-160475700	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr3:160471784-160475614	SK-N-SH	brain:	n/a	n/a
11	ZNF263	chr3:160472086-160475762	HEK293-T-REx	kidney:	n/a	n/a
12	POLR2A	chr3:160475050-160475525	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr3:160475026-160475625	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr3:160475227-160475714	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUND	chr3:160475395-160475663	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:160475003-160475508	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBP	chr3:160475042-160475619	H1-hESC	embryonic stem cell:	n/a	n/a
18	RAD21	chr3:160475176-160475494	H1-hESC	embryonic stem cell:	n/a	n/a
19	SIN3A	chr3:160472033-160475826	H1-hESC	embryonic stem cell:	n/a	chr3:160474702-160474716

No.	Distal block	Cell Line	Cell type
1	chr3:160475234..160478424-chr3:160481295..160484751,3	MCF-7	breast:
2	chr3:160475052..160477817-chr3:160492377..160494723,2	MCF-7	breast:
3	chr3:160281928..160283694-chr3:160472203..160475526,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260572	TF binding region
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10513553	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12486979	0.81[EUR][1000 genomes]
rs12487861	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap]
rs13068380	0.88[EUR][1000 genomes]
rs1378654	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1378657	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs1378658	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403048	0.83[EUR][1000 genomes]
rs1598495	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1829716	0.89[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];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851378	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1902282	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1915929	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2049214	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2049215	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2886905	0.82[EUR][1000 genomes]
rs59542611	0.89[EUR][1000 genomes]
rs6775743	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap]
rs6781371	0.80[EUR][1000 genomes]
rs6794047	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6805905	0.82[EUR][1000 genomes]
rs718757	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes]
rs722871	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618640	0.84[ASN][1000 genomes]
rs7618832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7630250	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7634342	0.82[EUR][1000 genomes]
rs7640348	0.80[EUR][1000 genomes]
rs7642371	0.82[EUR][1000 genomes]
rs7643513	0.83[EUR][1000 genomes]
rs779058	0.83[ASN][1000 genomes]
rs959960	0.80[EUR][1000 genomes]
rs972909	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9814394	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9815499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833075	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9866566	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes]
rs9868489	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1455869	IFT80	cis	parietal	SCAN
rs1455869	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160471800-160476600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:160472000-160475600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:160472000-160475600	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr3:160472000-160475600	Active TSS	Gastric	stomach
5	chr3:160472000-160476200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:160472000-160476200	Active TSS	Psoas Muscle	Psoas
7	chr3:160472000-160477800	Active TSS	Brain Angular Gyrus	brain
8	chr3:160472000-160477800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:160472200-160475600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:160472200-160475800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:160472200-160477400	Active TSS	Fetal Brain Female	brain
12	chr3:160472200-160477800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr3:160472400-160475600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:160473400-160475800	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr3:160473600-160475600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr3:160473800-160476000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr3:160473800-160476000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:160474000-160475600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr3:160474000-160475600	Flanking Active TSS	Liver	Liver
20	chr3:160474000-160475600	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr3:160474000-160475600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr3:160474000-160475800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr3:160474000-160475800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:160474000-160475800	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr3:160474000-160476200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr3:160474200-160475600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:160474200-160475600	Bivalent/Poised TSS	Fetal Kidney	kidney
28	chr3:160474200-160475600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
29	chr3:160474200-160475600	Flanking Active TSS	Lung	lung
30	chr3:160474200-160475600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr3:160474200-160475800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
32	chr3:160474200-160475800	Flanking Active TSS	Right Ventricle	heart
33	chr3:160474200-160475800	Flanking Active TSS	Hela-S3	cervix
34	chr3:160474200-160476000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:160474200-160476200	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr3:160474200-160476200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr3:160474200-160476800	Flanking Active TSS	Dnd41	blood
38	chr3:160474400-160475800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:160474400-160475800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
40	chr3:160474600-160475600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:160474600-160475600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:160474600-160475600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr3:160474600-160475600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
44	chr3:160474600-160475800	Bivalent Enhancer	Fetal Lung	lung
45	chr3:160474600-160476000	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr3:160474800-160475600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:160474800-160475600	Flanking Active TSS	Stomach Mucosa	stomach
48	chr3:160474800-160475800	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr3:160474800-160476000	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr3:160475000-160475600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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