Variant report

Variant	rs4823085
Chromosome Location	chr22:30686226-30686227
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	chr22:30685723-30686994	GM12878	blood:	n/a	n/a
2	PML	chr22:30685241-30686822	GM12878	blood:	n/a	chr22:30685671-30685679
3	STAT3	chr22:30686110-30686244	MCF10A-Er-Src	breast:	n/a	n/a
4	ELF1	chr22:30686105-30686573	HepG2	liver:	n/a	chr22:30686341-30686352 chr22:30686339-30686352 chr22:30686341-30686352 chr22:30686511-30686523 chr22:30686342-30686351
5	POLR2A	chr22:30685235-30687312	GM12878	blood:	n/a	n/a
6	POLR2A	chr22:30685366-30688017	GM12892	blood:	n/a	n/a
7	POLR2A	chr22:30686220-30687132	GM12878	blood:	n/a	n/a
8	POLR2A	chr22:30685344-30687144	GM12878	blood:	n/a	n/a
9	POLR2A	chr22:30685268-30686959	GM18951	blood:	n/a	n/a
10	CHD2	chr22:30686215-30686297	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr22:30686160-30686310	HMEC	breast:	n/a	n/a
12	CTCF	chr22:30686080-30686230	GM12867	blood:	n/a	chr22:30686088-30686101
13	CTCF	chr22:30686200-30686350	GM12864	blood:	n/a	n/a
14	POLR2A	chr22:30686073-30686485	GM12892	blood:	n/a	n/a
15	NFATC1	chr22:30685265-30686335	GM12878	blood:	n/a	chr22:30685853-30685866
16	POLR2A	chr22:30685098-30686646	H1-hESC	embryonic stem cell:	n/a	n/a
17	RCOR1	chr22:30685285-30686404	GM12878	blood:	n/a	n/a
18	BCL3	chr22:30685237-30686243	GM12878	blood:	n/a	chr22:30685602-30685615 chr22:30685546-30685555 chr22:30685541-30685554 chr22:30685543-30685552 chr22:30685260-30685273 chr22:30685580-30685593 chr22:30685254-30685267 chr22:30685598-30685611
19	POLR2A	chr22:30685186-30686444	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr22:30685291-30687284	GM12892	blood:	n/a	n/a
21	POLR2A	chr22:30685327-30687530	GM18505	blood:	n/a	n/a
22	MTA3	chr22:30686202-30686765	GM12878	blood:	n/a	n/a
23	ELF1	chr22:30685761-30686701	MCF-7	breast:	n/a	chr22:30686341-30686352 chr22:30686339-30686352 chr22:30686341-30686352 chr22:30686511-30686523 chr22:30686342-30686351
24	POLR2A	chr22:30685249-30686464	MCF-7	breast:	n/a	n/a
25	ELF1	chr22:30685101-30687172	GM12878	blood:	n/a	chr22:30686341-30686352 chr22:30686339-30686352 chr22:30686341-30686352 chr22:30686511-30686523 chr22:30685584-30685593 chr22:30686342-30686351 chr22:30685383-30685396
26	RCOR1	chr22:30686189-30686248	HepG2	liver:	n/a	n/a
27	POLR2A	chr22:30686149-30686879	GM12891	blood:	n/a	n/a
28	POLR2A	chr22:30685305-30687090	GM15510	blood:	n/a	n/a
29	POLR2A	chr22:30685135-30686248	U87	brain:	n/a	n/a
30	MXI1	chr22:30684871-30687521	SK-N-SH	brain:	n/a	chr22:30685923-30685932
31	POLR2A	chr22:30685794-30687323	GM12878	blood:	n/a	n/a
32	ELF1	chr22:30686176-30686513	HepG2	liver:	n/a	chr22:30686341-30686352 chr22:30686339-30686352 chr22:30686341-30686352 chr22:30686342-30686351
33	POLR2A	chr22:30685778-30686514	HepG2	liver:	n/a	n/a
34	CTCF	chr22:30686100-30686250	GM12872	blood:	n/a	n/a
35	POLR2A	chr22:30685284-30687235	GM12878	blood:	n/a	n/a
36	CTCF	chr22:30686080-30686230	HRE	kidney:	n/a	chr22:30686088-30686101
37	POLR2A	chr22:30685064-30686254	U87	brain:	n/a	n/a
38	CTCF	chr22:30686100-30686250	GM12866	blood:	n/a	n/a
39	MXI1	chr22:30684896-30686578	IMR90	lung:	n/a	chr22:30685923-30685932
40	CTCF	chr22:30686120-30686270	NHDF-neo	bronchial:	n/a	n/a
41	ELF1	chr22:30686194-30686509	K562	blood:	n/a	chr22:30686341-30686352 chr22:30686339-30686352 chr22:30686341-30686352 chr22:30686342-30686351
42	POLR2A	chr22:30685223-30687351	GM12892	blood:	n/a	n/a
43	POLR2A	chr22:30685743-30686488	GM12891	blood:	n/a	n/a
44	RUNX3	chr22:30685939-30687014	GM12878	blood:	n/a	n/a
45	YY1	chr22:30685927-30686236	GM12878	blood:	n/a	chr22:30686095-30686106
46	RUNX3	chr22:30685778-30686598	GM12878	blood:	n/a	n/a
47	CHD2	chr22:30685341-30686750	GM12878	blood:	n/a	chr22:30686061-30686068
48	CTCF	chr22:30686100-30686250	GM12868	blood:	n/a	n/a
49	POLR2A	chr22:30685161-30687933	GM12878	blood:	n/a	n/a
50	MAZ	chr22:30685380-30686502	K562	blood:	n/a	chr22:30685833-30685843

No.	Distal block	Cell Line	Cell type
1	chr22:30684944..30687538-chr22:30739118..30741799,2	MCF-7	breast:
2	chr22:30684284..30686749-chr22:30752450..30754272,3	MCF-7	breast:
3	chr22:30681692..30688141-chr22:30720232..30725114,19	MCF-7	breast:
4	chr22:30685629..30687266-chr22:30839148..30841021,2	K562	blood:
5	chr22:30679588..30687274-chr22:30748772..30756086,11	MCF-7	breast:
6	chr22:30681129..30691076-chr22:30751303..30759078,14	K562	blood:
7	chr22:30683198..30686724-chr22:30818649..30821641,4	K562	blood:
8	chr22:30683831..30686273-chr22:30722432..30724567,2	K562	blood:
9	chr22:30684219..30686932-chr22:30699973..30702656,2	MCF-7	breast:
10	chr22:30683076..30686857-chr22:30780059..30784684,12	MCF-7	breast:
11	chr22:30684393..30686613-chr22:30820961..30823363,3	MCF-7	breast:
12	chr22:30679348..30681690-chr22:30685966..30688546,2	K562	blood:

Variant related genes	Relation type
GATSL3	TF binding region
ENSG00000187860	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000099995	Chromatin interaction
ENSG00000099999	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10427610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1043099	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2041199	0.89[AMR][1000 genomes]
rs2108093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299830	0.86[ASN][1000 genomes]
rs4339043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4820844	0.80[ASN][1000 genomes]
rs5749066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749082	0.98[ASN][1000 genomes]
rs5753071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753088	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753111	0.98[ASN][1000 genomes]
rs737950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs740219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs757869	0.82[ASN][1000 genomes]
rs929454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9608904	0.90[ASN][1000 genomes]
rs9619104	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers 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
3	nsv914969	chr22:30619599-30691631	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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
6	nsv914971	chr22:30640308-30691631	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv914972	chr22:30640308-30693581	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	esv1799458	chr22:30659798-30698035	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv588885	chr22:30661184-30691631	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv522605	chr22:30685076-30691631	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4823085	SF3A1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30683600-30686800	Flanking Active TSS	Dnd41	blood
2	chr22:30684000-30686400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr22:30684000-30686600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr22:30684600-30686400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr22:30684800-30686400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr22:30685000-30686400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr22:30685800-30686400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr22:30685800-30686400	Flanking Active TSS	Primary B cells from peripheral blood	blood
9	chr22:30685800-30686400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr22:30685800-30686400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr22:30685800-30686400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr22:30685800-30686400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr22:30685800-30686400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr22:30685800-30686400	Flanking Active TSS	Colonic Mucosa	Colon
15	chr22:30685800-30686400	Flanking Active TSS	Fetal Thymus	thymus
16	chr22:30685800-30686400	Flanking Active TSS	Hela-S3	cervix
17	chr22:30685800-30686400	Flanking Active TSS	HSMM	muscle
18	chr22:30685800-30686400	Flanking Active TSS	Osteobl	bone
19	chr22:30685800-30686600	Flanking Active TSS	NHEK	skin
20	chr22:30685800-30686800	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr22:30685800-30686800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr22:30685800-30687200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr22:30685800-30687200	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr22:30685800-30687400	Enhancers	HSMMtube	muscle
25	chr22:30685800-30687800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr22:30686000-30686400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr22:30686000-30686400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr22:30686000-30686400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr22:30686000-30686400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr22:30686000-30686400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr22:30686000-30686400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr22:30686000-30686400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr22:30686000-30686400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr22:30686000-30686400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr22:30686000-30686400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr22:30686000-30686400	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr22:30686000-30686400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr22:30686000-30686400	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr22:30686000-30686400	Flanking Active TSS	GM12878-XiMat	blood
40	chr22:30686000-30686400	Flanking Active TSS	K562	blood
41	chr22:30686000-30686600	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr22:30686000-30686600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr22:30686000-30686600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr22:30686000-30686800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr22:30686000-30686800	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr22:30686000-30686800	Flanking Active TSS	HepG2	liver
47	chr22:30686000-30687000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr22:30686000-30687000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr22:30686000-30687200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr22:30686000-30687400	Flanking Active TSS	Colon Smooth Muscle	Colon

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