Variant report

Variant	rs66522549
Chromosome Location	chr1:221910411-221910412
allele	C/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	POLR2A	chr1:221910405-221910900	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:221909168-221918546	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:221909243-221918347	GM12878	blood:	n/a	n/a
4	ATF1	chr1:221910121-221910432	K562	blood:	n/a	n/a
5	POLR2A	chr1:221909298-221917710	GM12878	blood:	n/a	n/a
6	TBP	chr1:221909812-221910429	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:221910053-221910488	K562	blood:	n/a	n/a
8	POLR2A	chr1:221905289-221917384	K562	blood:	n/a	n/a
9	POLR2A	chr1:221910189-221910565	GM12891	blood:	n/a	n/a
10	EBF1	chr1:221909759-221910582	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:221910344-221910724	HepG2	liver:	n/a	n/a
12	MXI1	chr1:221910180-221910709	GM12878	blood:	n/a	n/a
13	WRNIP1	chr1:221909432-221910735	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:221910106-221910666	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:221909055-221918437	GM12891	blood:	n/a	n/a
16	JUND	chr1:221910156-221910413	K562	blood:	n/a	n/a
17	POLR2A	chr1:221909363-221918298	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
DUSP10	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10218652	0.82[AMR][1000 genomes]
rs10863653	0.82[AMR][1000 genomes]
rs10863654	0.82[AMR][1000 genomes]
rs11118844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118847	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11118848	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11118854	0.80[AMR][1000 genomes]
rs12070192	0.82[AMR][1000 genomes]
rs12144586	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12403995	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17010720	0.82[AMR][1000 genomes]
rs4433402	0.82[AMR][1000 genomes]
rs4589119	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4601596	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58850477	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6655994	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7516292	0.85[AMR][1000 genomes]
rs7518806	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking 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 target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221891800-221911000	Weak transcription	Gastric	stomach
2	chr1:221891800-221913000	Weak transcription	Fetal Intestine Large	intestine
3	chr1:221893000-221913600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:221897200-221914200	Weak transcription	Aorta	Aorta
5	chr1:221897400-221913400	Weak transcription	HepG2	liver
6	chr1:221898600-221913600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:221899400-221912400	Weak transcription	Esophagus	oesophagus
8	chr1:221899600-221912400	Weak transcription	Thymus	Thymus
9	chr1:221899800-221910800	Weak transcription	NH-A	brain
10	chr1:221900200-221911200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:221901400-221913800	Weak transcription	Placenta	Placenta
12	chr1:221901800-221913600	Weak transcription	Hela-S3	cervix
13	chr1:221901800-221913800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:221902600-221911200	Weak transcription	NHEK	skin
15	chr1:221903800-221912400	Weak transcription	Fetal Intestine Small	intestine
16	chr1:221904000-221911200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:221904000-221911200	Weak transcription	Fetal Stomach	stomach
18	chr1:221904000-221912400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:221904000-221912600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:221904000-221913800	Weak transcription	Ovary	ovary
21	chr1:221905800-221913400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:221906400-221912400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:221906400-221913000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:221907400-221910800	Enhancers	Psoas Muscle	Psoas
25	chr1:221907600-221910800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:221907600-221912600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:221907600-221912800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:221907600-221913600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
29	chr1:221907800-221913200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:221908200-221910800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:221908200-221911200	Weak transcription	Primary B cells from cord blood	blood
32	chr1:221908400-221911600	Active TSS	Fetal Brain Female	brain
33	chr1:221908400-221913000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
34	chr1:221908600-221910800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:221908600-221911000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:221908600-221912200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:221908600-221913400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:221908800-221911000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:221908800-221911200	Active TSS	Brain Angular Gyrus	brain
40	chr1:221908800-221913000	Genic enhancers	Monocytes-CD14+_RO01746	blood
41	chr1:221908800-221913200	Weak transcription	Fetal Heart	heart
42	chr1:221909000-221912800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
43	chr1:221909000-221913000	Genic enhancers	Primary monocytes fromperipheralblood	blood
44	chr1:221909000-221913400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:221909200-221910800	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr1:221909200-221912400	Genic enhancers	Pancreas	Pancrea
47	chr1:221909200-221913000	Transcr. at gene 5' and 3'	Liver	Liver
48	chr1:221909200-221913200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
49	chr1:221909200-221913400	Transcr. at gene 5' and 3'	HMEC	breast
50	chr1:221909400-221912400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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