Variant report

Variant	rs55851821
Chromosome Location	chr6:25138242-25138243
allele	A/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	chr6:25138223-25138841	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:25138023-25139021	GM12892	blood:	n/a	n/a
3	TCF12	chr6:25138111-25139011	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr6:25138179-25139227	SK-N-SH	brain:	n/a	n/a
5	MTA3	chr6:25137947-25139435	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:25137735-25138940	GM12892	blood:	n/a	n/a
7	STAT3	chr6:25138238-25139673	MCF10A-Er-Src	breast:	n/a	chr6:25139524-25139538 chr6:25139527-25139536 chr6:25139363-25139371 chr6:25139366-25139389 chr6:25139526-25139535 chr6:25139188-25139199 chr6:25138559-25138566 chr6:25139182-25139193
8	MAZ	chr6:25138151-25139330	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:25137762-25138962	GM12878	blood:	n/a	n/a
10	FOXM1	chr6:25138126-25139429	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:25137737-25139277	GM12892	blood:	n/a	n/a
12	SPI1	chr6:25138200-25138767	GM12878	blood:	n/a	chr6:25138561-25138568
13	TAF1	chr6:25138189-25138808	GM12878	blood:	n/a	n/a
14	ATF2	chr6:25137739-25139485	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:25137855-25138983	Raji	blood:	n/a	n/a
16	RELA	chr6:25137765-25139153	GM15510	blood:	n/a	n/a
17	SPI1	chr6:25137995-25139033	GM12878	blood:	n/a	chr6:25138561-25138568
18	CEBPB	chr6:25137782-25139143	IMR90	lung:	n/a	n/a
19	NFIC	chr6:25137751-25139570	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:25138234-25139009	GM12878	blood:	n/a	n/a
21	TBP	chr6:25138232-25139305	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:25137705-25138971	GM12892	blood:	n/a	n/a
23	POLR2A	chr6:25137863-25138925	NB4	blood:	n/a	n/a
24	STAT1	chr6:25138198-25138962	GM12878	blood:	n/a	chr6:25138559-25138566
25	MTA3	chr6:25138119-25139367	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:25136835-25139403	GM12891	blood:	n/a	n/a
27	NFATC1	chr6:25138105-25138907	GM12878	blood:	n/a	n/a
28	TAF1	chr6:25138203-25138758	GM12891	blood:	n/a	n/a
29	CEBPB	chr6:25137713-25139611	GM12878	blood:	n/a	n/a
30	RELA	chr6:25137773-25139379	GM19099	blood:	n/a	n/a
31	BATF	chr6:25138159-25138751	GM12878	blood:	n/a	n/a
32	FOS	chr6:25138194-25139210	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr6:25137453-25139116	GM12878	blood:	n/a	n/a
34	STAT5A	chr6:25138161-25139332	GM12878	blood:	n/a	chr6:25139188-25139199 chr6:25138559-25138566 chr6:25139182-25139193
35	POLR2A	chr6:25138240-25138921	Hela-S3	cervix:	n/a	n/a
36	FOXM1	chr6:25138117-25139412	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:25136992-25139613	MCF10A-Er-Src	breast:	n/a	n/a
38	ATF2	chr6:25138138-25139054	GM12878	blood:	n/a	n/a
39	CEBPB	chr6:25137779-25139523	Hela-S3	cervix:	n/a	n/a
40	WRNIP1	chr6:25137799-25138821	GM12878	blood:	n/a	n/a
41	POLR2A	chr6:25138201-25138905	GM12878	blood:	n/a	n/a
42	GATA1	chr6:25136718-25138791	PBDE	blood:	n/a	chr6:25137782-25137792
43	POLR2A	chr6:25138164-25138831	GM12891	blood:	n/a	n/a
44	TBL1XR1	chr6:25138169-25139353	GM12878	blood:	n/a	n/a
45	RUNX3	chr6:25138167-25139298	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:25138127-25138944	GM12891	blood:	n/a	n/a
47	POLR2A	chr6:25138032-25138854	GM12892	blood:	n/a	n/a
48	POLR2A	chr6:25138167-25138994	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr6:25138082-25138877	GM12891	blood:	n/a	n/a
50	SPI1	chr6:25138223-25138806	GM12891	blood:	n/a	chr6:25138561-25138568

Variant related genes	Relation type
CMAHP	TF binding region
ENSG00000219682	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs182499	0.86[ASN][1000 genomes]
rs188567	1.00[ASN][1000 genomes]
rs28539031	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302981	1.00[ASN][1000 genomes]
rs303003	0.86[ASN][1000 genomes]
rs303012	0.86[ASN][1000 genomes]
rs416030	0.86[ASN][1000 genomes]
rs57003751	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs59778363	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6908916	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73386265	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654578	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1798120	chr6:25136860-25149538	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25123800-25138400	Weak transcription	Pancreas	Pancrea
2	chr6:25135200-25140200	Active TSS	Right Atrium	heart
3	chr6:25136000-25138800	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr6:25136000-25139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:25136200-25139000	Active TSS	Left Ventricle	heart
6	chr6:25136200-25139600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr6:25136200-25139800	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr6:25136200-25140000	Active TSS	Aorta	Aorta
9	chr6:25136400-25139200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr6:25136400-25139400	Active TSS	Brain Hippocampus Middle	brain
11	chr6:25136600-25139400	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr6:25136600-25139600	Active TSS	Duodenum Mucosa	Duodenum
13	chr6:25136600-25140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:25136800-25138400	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr6:25136800-25138400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr6:25136800-25138800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:25136800-25138800	Active TSS	Sigmoid Colon	Sigmoid Colon
18	chr6:25136800-25139000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr6:25136800-25139000	Flanking Active TSS	Liver	Liver
20	chr6:25136800-25139000	Flanking Active TSS	Osteobl	bone
21	chr6:25136800-25139400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr6:25136800-25139400	Active TSS	Brain Anterior Caudate	brain
23	chr6:25136800-25139400	Active TSS	Right Ventricle	heart
24	chr6:25136800-25140000	Active TSS	Ovary	ovary
25	chr6:25137000-25138400	Enhancers	Fetal Stomach	stomach
26	chr6:25137000-25139000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:25137000-25139400	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr6:25137000-25139400	Active TSS	Colonic Mucosa	Colon
29	chr6:25137000-25139400	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr6:25137000-25139800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:25137000-25140200	Active TSS	Psoas Muscle	Psoas
32	chr6:25137200-25139600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:25137200-25139600	Active TSS	Rectal Smooth Muscle	rectum
34	chr6:25137400-25139400	Active TSS	Primary T cells fromperipheralblood	blood
35	chr6:25137400-25139400	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr6:25137400-25139400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr6:25137400-25139400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr6:25137400-25139400	Active TSS	Colon Smooth Muscle	Colon
39	chr6:25137400-25139400	Active TSS	GM12878-XiMat	blood
40	chr6:25137400-25139600	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr6:25137600-25138400	Active TSS	Small Intestine	intestine
42	chr6:25137600-25139400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:25137600-25139400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:25137600-25139400	Weak transcription	Fetal Heart	heart
45	chr6:25137600-25139600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:25137800-25138400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:25137800-25138400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr6:25137800-25138400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:25137800-25138400	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr6:25137800-25138400	Flanking Active TSS	HSMM	muscle

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