Variant report

Variant	rs66466805
Chromosome Location	chr1:155888666-155888667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155888434-155889367	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:155887563-155888749	K562	blood:	n/a	n/a
3	POLR2A	chr1:155888510-155889195	K562	blood:	n/a	n/a
4	POLR2A	chr1:155887544-155889563	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:155887546-155889171	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr1:155888524-155888819	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:155887508-155889294	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:155887637-155888865	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:155888417-155888819	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr1:155888602-155889005	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:155887881-155889200	GM12891	blood:	n/a	n/a
12	ZNF384	chr1:155888664-155888812	K562	blood:	n/a	n/a
13	POLR2A	chr1:155887589-155888778	GM12891	blood:	n/a	n/a
14	POLR2A	chr1:155888464-155888888	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr1:155888318-155888729	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr1:155887459-155888893	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr1:155887394-155889287	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:155888516-155888786	GM12891	blood:	n/a	n/a
19	POLR2A	chr1:155888160-155888693	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:155888535-155888738	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:155888440-155888821	GM12891	blood:	n/a	n/a
22	POLR2A	chr1:155887447-155888768	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:155888260-155888816	K562	blood:	n/a	n/a
24	GATA3	chr1:155888479-155888819	T-47D	breast:	n/a	n/a
25	POLR2A	chr1:155888487-155888678	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:155887531-155888850	MCF-7	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155879962..155882698-chr1:155885713..155888748,6	MCF-7	breast:
2	chr1:155886446..155889315-chr1:155891055..155892735,3	K562	blood:

No data

Variant related genes	Relation type
KIAA0907	TF binding region
ENSG00000132680	Chromatin interaction
ENSG00000143622	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10796955	0.82[AMR][1000 genomes]
rs10908483	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12026057	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037177	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12080846	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12091273	0.91[AFR][1000 genomes]
rs12091361	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12144175	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12568523	0.86[EUR][1000 genomes]
rs1889532	0.82[AMR][1000 genomes]
rs1889533	0.82[AMR][1000 genomes]
rs2016251	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2282301	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297649	0.82[AMR][1000 genomes]
rs2364403	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs66669006	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6667652	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6670477	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6696019	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72708205	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7528441	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7545308	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs867548	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867549	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867550	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs915181	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[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	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66466805	RIT1	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155881400-155889600	Weak transcription	Pancreas	Pancrea
2	chr1:155881400-155890400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:155881600-155889800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:155881600-155890800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:155881800-155893600	Strong transcription	HMEC	breast
6	chr1:155881800-155898800	Strong transcription	HUVEC	blood vessel
7	chr1:155881800-155899800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:155881800-155900600	Strong transcription	Fetal Muscle Leg	muscle
9	chr1:155881800-155901200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:155881800-155901200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:155882000-155888800	Strong transcription	Primary hematopoietic stem cells	blood
12	chr1:155882000-155898800	Strong transcription	NH-A	brain
13	chr1:155882000-155899400	Strong transcription	Fetal Intestine Large	intestine
14	chr1:155882000-155899800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:155882000-155900000	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:155882000-155900000	Strong transcription	Liver	Liver
17	chr1:155882000-155900200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:155882000-155900400	Strong transcription	Primary B cells from cord blood	blood
19	chr1:155882000-155900600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:155882000-155900600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:155882000-155900600	Strong transcription	Placenta	Placenta
22	chr1:155882000-155900600	Strong transcription	Fetal Stomach	stomach
23	chr1:155882000-155900600	Strong transcription	Left Ventricle	heart
24	chr1:155882000-155900800	Strong transcription	Thymus	Thymus
25	chr1:155882000-155901000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:155882000-155901400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:155882000-155901400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:155882200-155898600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:155882200-155900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:155882200-155900600	Strong transcription	Fetal Thymus	thymus
31	chr1:155882200-155901000	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:155882200-155901000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:155882200-155901200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:155882200-155901400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:155882200-155901400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr1:155882200-155901400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:155882200-155903000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:155882400-155893800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:155882400-155898800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:155882400-155900000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:155882400-155900000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:155882400-155900000	Strong transcription	Adipose Nuclei	Adipose
43	chr1:155882400-155900200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:155882600-155888800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:155882600-155889400	Strong transcription	Colon Smooth Muscle	Colon
46	chr1:155882600-155898800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:155882600-155899000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:155882600-155899000	Strong transcription	NHEK	skin
49	chr1:155882600-155900200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:155882600-155900200	Strong transcription	Skeletal Muscle Female	skeletal muscle

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