Variant report

Variant	rs2582532
Chromosome Location	chr14:105392837-105392838
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	IRF4	chr14:105392786-105393310	GM12878	blood:	n/a	n/a
2	EBF1	chr14:105392553-105393550	GM12878	blood:	n/a	n/a
3	NFIC	chr14:105392719-105393389	GM12878	blood:	n/a	n/a
4	SP1	chr14:105392792-105393290	GM12878	blood:	n/a	n/a
5	ATF2	chr14:105392833-105393230	GM12878	blood:	n/a	n/a
6	MEF2C	chr14:105392747-105393279	GM12878	blood:	n/a	chr14:105392992-105393001 chr14:105392990-105393001 chr14:105392987-105393008 chr14:105392991-105393002
7	FOXM1	chr14:105392741-105393341	GM12878	blood:	n/a	n/a
8	STAT5A	chr14:105392481-105393382	GM12878	blood:	n/a	n/a
9	NFATC1	chr14:105392776-105393272	GM12878	blood:	n/a	n/a
10	RUNX3	chr14:105392558-105393517	GM12878	blood:	n/a	n/a
11	ELF1	chr14:105392659-105393662	GM12878	blood:	n/a	n/a
12	CTCF	chr14:105392700-105392850	GM12872	blood:	n/a	n/a
13	CTCF	chr14:105392816-105392899	H1-hESC	embryonic stem cell:	n/a	n/a
14	SPI1	chr14:105392535-105393485	GM12878	blood:	n/a	chr14:105393077-105393086
15	BCL3	chr14:105392796-105393270	GM12878	blood:	n/a	chr14:105393077-105393086
16	RELA	chr14:105392693-105393305	GM19193	blood:	n/a	n/a
17	NFATC1	chr14:105392836-105393277	GM12878	blood:	n/a	n/a
18	POU2F2	chr14:105392738-105393382	GM12878	blood:	n/a	chr14:105393086-105393093 chr14:105393078-105393100
19	POU2F2	chr14:105392766-105393420	GM12891	blood:	n/a	chr14:105393086-105393093 chr14:105393078-105393100
20	CTCF	chr14:105392789-105392899	GM12891	blood:	n/a	n/a
21	CTCF	chr14:105392700-105392850	GM12867	blood:	n/a	n/a
22	TBL1XR1	chr14:105392820-105393373	GM12878	blood:	n/a	n/a
23	RELA	chr14:105392773-105393290	GM10847	blood:	n/a	n/a
24	MAZ	chr14:105392702-105393389	GM12878	blood:	n/a	n/a
25	PML	chr14:105392718-105393353	GM12878	blood:	n/a	n/a
26	POLR2A	chr14:105392089-105393339	GM19193	blood:	n/a	n/a
27	BHLHE40	chr14:105392796-105393418	GM12878	blood:	n/a	n/a
28	CHD2	chr14:105392827-105393412	GM12878	blood:	n/a	n/a
29	MTA3	chr14:105392799-105393357	GM12878	blood:	n/a	n/a
30	CTCF	chr14:105392720-105392870	WERI-Rb-1	eye:	n/a	n/a
31	RELA	chr14:105392678-105393247	GM15510	blood:	n/a	n/a
32	BCLAF1	chr14:105392803-105393399	GM12878	blood:	n/a	chr14:105393266-105393279 chr14:105393077-105393086
33	BCLAF1	chr14:105392732-105393342	GM12878	blood:	n/a	chr14:105393266-105393279 chr14:105393077-105393086
34	PAX5	chr14:105392705-105393437	GM12878	blood:	n/a	chr14:105393077-105393086
35	MEF2A	chr14:105392813-105393412	GM12878	blood:	n/a	chr14:105392992-105393001 chr14:105392990-105393001 chr14:105392987-105393008 chr14:105392991-105393002
36	POU2F2	chr14:105392757-105393316	GM12891	blood:	n/a	chr14:105393086-105393093 chr14:105393078-105393100
37	SPI1	chr14:105392806-105393219	GM12891	blood:	n/a	chr14:105393077-105393086
38	POU2F2	chr14:105392795-105393332	GM12878	blood:	n/a	chr14:105393086-105393093 chr14:105393078-105393100
39	RCOR1	chr14:105392731-105393384	GM12878	blood:	n/a	n/a
40	MTA3	chr14:105390644-105393638	GM12878	blood:	n/a	n/a
41	MEF2C	chr14:105392667-105393339	GM12878	blood:	n/a	chr14:105392992-105393001 chr14:105392990-105393001 chr14:105392987-105393008 chr14:105392991-105393002
42	RUNX3	chr14:105392652-105393530	GM12878	blood:	n/a	n/a
43	CEBPB	chr14:105392767-105393371	GM12878	blood:	n/a	n/a
44	FOXM1	chr14:105392734-105393274	GM12878	blood:	n/a	n/a
45	CTCF	chr14:105392740-105392890	GM12873	blood:	n/a	n/a
46	MEF2A	chr14:105392624-105393392	GM12878	blood:	n/a	chr14:105392992-105393001 chr14:105392990-105393001 chr14:105392987-105393008 chr14:105392991-105393002
47	EBF1	chr14:105392588-105393388	GM12878	blood:	n/a	n/a
48	ATF2	chr14:105392794-105393346	GM12878	blood:	n/a	n/a
49	EP300	chr14:105392760-105393444	GM12878	blood:	n/a	chr14:105393072-105393086
50	IRF4	chr14:105392735-105393310	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:105387983..105391489-chr14:105392006..105395629,4	MCF-7	breast:
2	chr14:105391507..105394096-chr14:105419228..105421927,2	MCF-7	breast:
3	chr14:105391640..105393998-chr14:105436679..105438519,2	MCF-7	breast:
4	chr14:105387917..105389579-chr14:105391282..105393689,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AHNAK2-2	chr14:105392628-105392969	expReg_chr14_7321_-

Variant related genes	Relation type
PLD4	TF binding region
ENSG00000185567	Chromatin interaction
ENSG00000166428	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2582530	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2819464	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3001423	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053591	chr14:105024558-105475931	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv542224	chr14:105024558-105475931	Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1828345	chr14:105100787-105803170	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
4	nsv542225	chr14:105133688-105803170	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
5	nsv542227	chr14:105157572-105803170	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
6	nsv456456	chr14:105285159-105412541	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv566099	chr14:105285159-105412541	Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS 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	38 gene(s)	inside rSNPs	diseases
8	nsv917106	chr14:105339195-105803170	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv566139	chr14:105347296-105417147	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv902419	chr14:105381763-105494262	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1049253	chr14:105384959-105471855	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv542228	chr14:105390569-105459912	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Rheumatoid arthritis	24390342	GWAS catalog

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105390800-105393600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr14:105390800-105393600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr14:105390800-105393600	Flanking Active TSS	GM12878-XiMat	blood
4	chr14:105390800-105393600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr14:105390800-105394000	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr14:105391000-105393200	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr14:105391000-105394000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr14:105391000-105395400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:105391200-105393000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr14:105391200-105393600	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr14:105391200-105393600	Enhancers	Adipose Nuclei	Adipose
12	chr14:105391200-105393600	Active TSS	Brain Hippocampus Middle	brain
13	chr14:105391200-105394200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr14:105391600-105393000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:105391600-105394200	Enhancers	Fetal Thymus	thymus
16	chr14:105391600-105395000	Enhancers	Fetal Intestine Small	intestine
17	chr14:105391600-105398600	Weak transcription	Gastric	stomach
18	chr14:105391800-105394200	Enhancers	Spleen	Spleen
19	chr14:105392200-105393000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr14:105392200-105393000	Enhancers	NH-A	brain
21	chr14:105392200-105394200	Enhancers	Fetal Muscle Leg	muscle
22	chr14:105392200-105395800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr14:105392600-105393000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr14:105392600-105393000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr14:105392600-105393000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:105392600-105393000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr14:105392600-105393000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr14:105392600-105393600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
29	chr14:105392600-105393800	Weak transcription	Fetal Intestine Large	intestine
30	chr14:105392600-105394400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr14:105392600-105394600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr14:105392800-105393200	Active TSS	Duodenum Mucosa	Duodenum
33	chr14:105392800-105393400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr14:105392800-105393600	Enhancers	Placenta	Placenta
35	chr14:105392800-105393800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr14:105392800-105393800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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