Variant report

Variant	rs879580
Chromosome Location	chr22:29659960-29659961
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:29659952-29660137	HepG2	liver:	n/a	n/a
2	POLR2A	chr22:29659624-29660768	K562	blood:	n/a	n/a
3	POLR2A	chr22:29659478-29660841	GM12878	blood:	n/a	n/a
4	POLR2A	chr22:29659859-29660343	A549	lung:	n/a	n/a
5	POLR2A	chr22:29659603-29660492	GM12891	blood:	n/a	n/a
6	POLR2A	chr22:29658533-29660725	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr22:29659914-29660331	MCF-7	breast:	n/a	n/a
8	POLR2A	chr22:29659687-29660366	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr22:29659835-29660221	A549	lung:	n/a	n/a
10	HMGN3	chr22:29659827-29660120	K562	blood:	n/a	n/a
11	POLR2A	chr22:29659571-29660488	GM12891	blood:	n/a	n/a
12	POLR2A	chr22:29659930-29660301	GM12878	blood:	n/a	n/a
13	POLR2A	chr22:29659543-29660706	GM12891	blood:	n/a	n/a
14	POLR2A	chr22:29659694-29660342	GM12878	blood:	n/a	n/a
15	POLR2A	chr22:29659615-29660151	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr22:29659835-29660471	HL-60	blood:	n/a	n/a
17	POLR2A	chr22:29659551-29660515	K562	blood:	n/a	n/a
18	POLR2A	chr22:29659502-29660728	K562	blood:	n/a	n/a
19	POLR2A	chr22:29659463-29660685	GM12892	blood:	n/a	n/a
20	POLR2A	chr22:29659767-29660200	GM12878	blood:	n/a	n/a
21	POLR2A	chr22:29659921-29660375	GM12892	blood:	n/a	n/a
22	POLR2A	chr22:29654506-29660719	HepG2	liver:	n/a	n/a
23	POLR2A	chr22:29659656-29660430	GM19193	blood:	n/a	n/a
24	POLR2A	chr22:29659440-29660763	GM12892	blood:	n/a	n/a
25	POLR2A	chr22:29659852-29660315	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr22:29659623-29660654	GM12878	blood:	n/a	n/a
27	POLR2A	chr22:29659599-29660551	GM12892	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29654217..29657445-chr22:29658284..29661902,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RASL10A-3	chr22:29659824-29660390	NONHSAT084684

No data

Variant related genes	Relation type
EWSR1	TF binding region
ENSG00000237015	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11090564	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs131180	0.88[ASN][1000 genomes]
rs131182	0.85[ASN][1000 genomes]
rs131189	0.82[ASN][1000 genomes]
rs140062	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs140063	0.88[ASN][1000 genomes]
rs140066	0.83[ASN][1000 genomes]
rs174759	0.86[ASN][1000 genomes]
rs174761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs174762	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs174764	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs174766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs174770	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs2071578	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2072051	0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2267132	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2267133	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs2283849	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2283850	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs2301290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301291	0.80[JPT][hapmap]
rs2301585	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2857462	0.81[ASN][1000 genomes]
rs2857466	0.89[JPT][hapmap]
rs28755	0.84[ASN][1000 genomes]
rs3788410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[ASN][1000 genomes]
rs3788411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4820803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs5752903	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs5763138	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs5763139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[ASN][1000 genomes]
rs6006090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6006098	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs715494	0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs737883	0.80[JPT][hapmap]
rs762817	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs909798	0.84[JPT][hapmap]
rs9537	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs98069	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv1809952	chr22:29595349-29661434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29641600-29661800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr22:29642600-29662400	Strong transcription	Fetal Intestine Small	intestine
3	chr22:29643600-29660400	Weak transcription	Fetal Kidney	kidney
4	chr22:29647400-29662000	Strong transcription	Fetal Stomach	stomach
5	chr22:29649000-29662400	Weak transcription	Fetal Brain Male	brain
6	chr22:29650200-29662600	Weak transcription	Stomach Mucosa	stomach
7	chr22:29650600-29660000	Weak transcription	Primary T cells from cord blood	blood
8	chr22:29650600-29660200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr22:29651000-29660000	Weak transcription	HepG2	liver
10	chr22:29652400-29660200	Weak transcription	NHEK	skin
11	chr22:29653600-29662200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr22:29654200-29662600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr22:29654400-29660000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr22:29654600-29662200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr22:29654600-29662400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr22:29654600-29662400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr22:29654600-29662600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr22:29654800-29662400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr22:29655200-29661200	Weak transcription	GM12878-XiMat	blood
20	chr22:29655600-29662800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr22:29657000-29660000	Weak transcription	Colonic Mucosa	Colon
22	chr22:29657000-29660000	Weak transcription	Left Ventricle	heart
23	chr22:29657200-29660000	Weak transcription	Brain Angular Gyrus	brain
24	chr22:29657200-29660000	Weak transcription	HSMMtube	muscle
25	chr22:29657800-29660000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr22:29658000-29661200	Weak transcription	NHDF-Ad	bronchial
27	chr22:29658200-29662200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr22:29658200-29662200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr22:29658200-29662400	Weak transcription	Right Atrium	heart
30	chr22:29658400-29660000	Weak transcription	K562	blood
31	chr22:29658400-29662800	Weak transcription	Primary B cells from cord blood	blood
32	chr22:29658600-29660400	Weak transcription	HUVEC	blood vessel
33	chr22:29658600-29662600	Weak transcription	Psoas Muscle	Psoas
34	chr22:29658800-29661400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr22:29659200-29662000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr22:29659400-29661400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr22:29659400-29661400	Strong transcription	Brain Anterior Caudate	brain
38	chr22:29659400-29662000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr22:29659400-29662000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr22:29659400-29662000	Weak transcription	Hela-S3	cervix
41	chr22:29659600-29660000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr22:29659600-29660200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr22:29659600-29660200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr22:29659600-29660200	Genic enhancers	Spleen	Spleen
45	chr22:29659600-29661000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
46	chr22:29659600-29661000	Strong transcription	HSMM	muscle
47	chr22:29659600-29661400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr22:29659600-29661400	Strong transcription	Fetal Lung	lung
49	chr22:29659600-29661400	Strong transcription	Dnd41	blood
50	chr22:29659600-29661600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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