Variant report

Variant	rs2841277
Chromosome Location	chr14:105391005-105391006
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	SPI1	chr14:105390990-105391332	GM12891	blood:	n/a	chr14:105391159-105391168 chr14:105391160-105391167 chr14:105391156-105391169 chr14:105391157-105391170
2	RUNX3	chr14:105390790-105391406	GM12878	blood:	n/a	n/a
3	SPI1	chr14:105390564-105391441	HL-60	blood:	n/a	chr14:105391159-105391168 chr14:105391160-105391167 chr14:105391156-105391169 chr14:105391157-105391170
4	ELF1	chr14:105390753-105391913	GM12878	blood:	n/a	n/a
5	STAT5A	chr14:105390454-105391044	GM12878	blood:	n/a	chr14:105390515-105390527
6	MTA3	chr14:105390644-105393638	GM12878	blood:	n/a	n/a
7	SPI1	chr14:105390898-105391346	GM12891	blood:	n/a	chr14:105391159-105391168 chr14:105391160-105391167 chr14:105391156-105391169 chr14:105391157-105391170
8	POLR2A	chr14:105390817-105391951	GM12891	blood:	n/a	n/a
9	ELF1	chr14:105390971-105391390	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:105389558..105391968-chr14:105443207..105445217,2	MCF-7	breast:

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

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10083374	0.84[AMR][1000 genomes]
rs10083490	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes]
rs10083496	0.87[AMR][1000 genomes]
rs10149193	0.85[AMR][1000 genomes]
rs10152073	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1036713	0.95[CHB][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10438246	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1048257	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes]
rs11623422	0.94[CHB][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs11851053	0.95[CHB][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs12885004	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2582529	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2582530	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs2582531	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582533	0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2819419	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2819422	0.85[AMR][1000 genomes]
rs2819424	0.84[AMR][1000 genomes]
rs2819439	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2819468	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2819469	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28380382	0.81[AMR][1000 genomes]
rs2841268	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2841269	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2841276	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2841278	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2841280	0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2841281	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28454709	0.83[AMR][1000 genomes]
rs28600075	0.83[AMR][1000 genomes]
rs2919624	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001424	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742935	0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4264326	0.81[AMR][1000 genomes]
rs4465542	0.83[AMR][1000 genomes]
rs61996025	0.81[AMR][1000 genomes]
rs874753	0.82[EUR][1000 genomes]
rs879448	0.83[EUR][1000 genomes]
rs9671643	0.83[AMR][1000 genomes]
rs9672139	0.89[AMR][1000 genomes];0.90[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	22446963	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2841277	AHNAK2	cis	cerebellum	SCAN
rs2841277	SLC25A47	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105389200-105391200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr14:105389400-105391200	Enhancers	Primary B cells from peripheral blood	blood
3	chr14:105390000-105391200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr14:105390200-105391600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:105390400-105391200	ZNF genes & repeats	Spleen	Spleen
6	chr14:105390800-105391200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
7	chr14:105390800-105392600	Enhancers	Placenta	Placenta
8	chr14:105390800-105393600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr14:105390800-105393600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr14:105390800-105393600	Flanking Active TSS	GM12878-XiMat	blood
11	chr14:105390800-105393600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr14:105390800-105394000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr14:105391000-105391200	Enhancers	Fetal Thymus	thymus
14	chr14:105391000-105391400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:105391000-105392000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr14:105391000-105392200	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr14:105391000-105393200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr14:105391000-105394000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr14:105391000-105395400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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