Variant report

Variant	rs311566
Chromosome Location	chr2:86294411-86294412
allele	A/T
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	EP300	chr2:86292386-86294615	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr2:86294287-86294531	SH-SY5Y	brain:	n/a	chr2:86294474-86294481
3	MAFK	chr2:86294072-86294495	HepG2	liver:	n/a	chr2:86294267-86294282
4	MAFK	chr2:86294081-86294596	IMR90	lung:	n/a	chr2:86294267-86294282
5	MAFF	chr2:86294083-86294549	HepG2	liver:	n/a	chr2:86294265-86294283
6	MAFK	chr2:86294093-86294542	HepG2	liver:	n/a	chr2:86294267-86294282

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86283452..86286024-chr2:86293941..86297049,3	MCF-7	breast:

Variant related genes	Relation type
POLR1A	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10165327	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10174095	0.83[ASN][1000 genomes]
rs10179090	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1019591	0.89[ASN][1000 genomes]
rs1036554	0.83[ASN][1000 genomes]
rs10427394	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11899576	0.83[ASN][1000 genomes]
rs12612513	0.89[ASN][1000 genomes]
rs12614260	0.89[ASN][1000 genomes]
rs12622009	0.84[ASN][1000 genomes]
rs13384563	0.81[ASN][1000 genomes]
rs13390702	0.83[ASN][1000 genomes]
rs1559516	0.96[ASN][1000 genomes]
rs1561328	0.87[ASN][1000 genomes]
rs17026854	0.87[ASN][1000 genomes]
rs17584578	0.89[ASN][1000 genomes]
rs17618001	0.89[ASN][1000 genomes]
rs2164879	0.84[ASN][1000 genomes]
rs2241437	0.85[ASN][1000 genomes]
rs2278085	0.87[ASN][1000 genomes]
rs2278087	0.89[ASN][1000 genomes]
rs2278088	0.89[ASN][1000 genomes]
rs2288121	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2289237	0.84[ASN][1000 genomes]
rs2303340	0.87[ASN][1000 genomes]
rs311562	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311563	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs311565	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs311567	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311569	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs311570	0.97[AFR][1000 genomes]
rs311571	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs311572	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs311573	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs311587	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3731819	0.86[ASN][1000 genomes]
rs3770073	0.94[AFR][1000 genomes]
rs3770081	0.82[ASN][1000 genomes]
rs3770087	0.84[ASN][1000 genomes]
rs3770089	0.84[ASN][1000 genomes]
rs3770090	0.84[ASN][1000 genomes]
rs3810827	0.87[ASN][1000 genomes]
rs3810828	0.90[AFR][1000 genomes]
rs3815840	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832021	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4832027	0.88[AFR][1000 genomes]
rs4832242	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4832250	0.96[ASN][1000 genomes]
rs56104203	0.87[ASN][1000 genomes]
rs57083584	0.89[ASN][1000 genomes]
rs57398459	0.89[ASN][1000 genomes]
rs60649958	0.89[ASN][1000 genomes]
rs6715623	0.90[AFR][1000 genomes]
rs6750765	0.86[ASN][1000 genomes]
rs73943946	0.83[ASN][1000 genomes]
rs73947314	0.87[ASN][1000 genomes]
rs7608262	0.82[ASN][1000 genomes]
rs9789563	0.87[ASN][1000 genomes]
rs979940	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs311566	POLR1A	cis	Esophagus Muscularis	GTEx
rs311566	POLR1A	cis	Artery Tibial	GTEx
rs311566	MRPL35	cis	Esophagus Muscularis	GTEx
rs311566	POLR1A	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:86265800-86305400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:86266400-86295800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:86268800-86295000	Strong transcription	Dnd41	blood
7	chr2:86282600-86299200	Weak transcription	Small Intestine	intestine
8	chr2:86282800-86295800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:86285800-86294600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:86285800-86299400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:86286000-86302200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:86286000-86331000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:86286000-86331200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:86286200-86298400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:86286200-86298600	Strong transcription	Fetal Lung	lung
16	chr2:86286200-86310400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:86286200-86311200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:86287000-86298800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:86287200-86294600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr2:86289800-86296000	Weak transcription	Stomach Mucosa	stomach
21	chr2:86289800-86307200	Strong transcription	HepG2	liver
22	chr2:86290200-86295600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:86290200-86299400	Strong transcription	Hela-S3	cervix
24	chr2:86290200-86310800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:86290600-86297600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:86290600-86306200	Strong transcription	Fetal Intestine Large	intestine
27	chr2:86290800-86298200	Strong transcription	Liver	Liver
28	chr2:86290800-86299400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr2:86290800-86310200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:86290800-86314600	Strong transcription	HMEC	breast
31	chr2:86290800-86318600	Strong transcription	K562	blood
32	chr2:86290800-86322600	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr2:86291000-86298400	Strong transcription	Primary B cells from cord blood	blood
34	chr2:86291000-86311200	Strong transcription	Fetal Brain Female	brain
35	chr2:86291400-86299200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:86291600-86295200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:86291600-86295200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:86291600-86297600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:86291600-86319000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:86291800-86295200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:86291800-86295200	Strong transcription	A549	lung
42	chr2:86291800-86295200	Strong transcription	Osteobl	bone
43	chr2:86291800-86298000	Weak transcription	Fetal Brain Male	brain
44	chr2:86291800-86298800	Strong transcription	HUVEC	blood vessel
45	chr2:86291800-86299400	Strong transcription	GM12878-XiMat	blood
46	chr2:86291800-86311400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:86291800-86318800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:86292000-86298600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:86292000-86298600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr2:86292400-86294800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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