Variant report

Variant	rs57003751
Chromosome Location	chr6:25138153-25138154
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	chr6:25138023-25139021	GM12892	blood:	n/a	n/a
2	TCF12	chr6:25138111-25139011	SK-N-SH	brain:	n/a	n/a
3	MTA3	chr6:25137947-25139435	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:25137735-25138940	GM12892	blood:	n/a	n/a
5	MAZ	chr6:25138151-25139330	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:25137762-25138962	GM12878	blood:	n/a	n/a
7	FOXM1	chr6:25138126-25139429	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:25137737-25139277	GM12892	blood:	n/a	n/a
9	ATF2	chr6:25137739-25139485	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:25137855-25138983	Raji	blood:	n/a	n/a
11	RELA	chr6:25137765-25139153	GM15510	blood:	n/a	n/a
12	SPI1	chr6:25137995-25139033	GM12878	blood:	n/a	chr6:25138561-25138568
13	CEBPB	chr6:25137782-25139143	IMR90	lung:	n/a	n/a
14	NFIC	chr6:25137751-25139570	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:25137705-25138971	GM12892	blood:	n/a	n/a
16	POLR2A	chr6:25137863-25138925	NB4	blood:	n/a	n/a
17	MTA3	chr6:25138119-25139367	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:25136835-25139403	GM12891	blood:	n/a	n/a
19	NFATC1	chr6:25138105-25138907	GM12878	blood:	n/a	n/a
20	CEBPB	chr6:25137713-25139611	GM12878	blood:	n/a	n/a
21	RELA	chr6:25137773-25139379	GM19099	blood:	n/a	n/a
22	POLR2A	chr6:25137453-25139116	GM12878	blood:	n/a	n/a
23	FOXM1	chr6:25138117-25139412	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:25136992-25139613	MCF10A-Er-Src	breast:	n/a	n/a
25	ATF2	chr6:25138138-25139054	GM12878	blood:	n/a	n/a
26	CEBPB	chr6:25137779-25139523	Hela-S3	cervix:	n/a	n/a
27	WRNIP1	chr6:25137799-25138821	GM12878	blood:	n/a	n/a
28	GATA1	chr6:25136718-25138791	PBDE	blood:	n/a	chr6:25137782-25137792
29	POLR2A	chr6:25138127-25138944	GM12891	blood:	n/a	n/a
30	POLR2A	chr6:25138032-25138854	GM12892	blood:	n/a	n/a
31	POLR2A	chr6:25138082-25138877	GM12891	blood:	n/a	n/a
32	POLR2A	chr6:25138130-25138897	GM12891	blood:	n/a	n/a
33	ELF1	chr6:25138101-25138805	GM12878	blood:	n/a	n/a
34	POU2F2	chr6:25138135-25139089	GM12878	blood:	n/a	n/a
35	PML	chr6:25137629-25139385	GM12878	blood:	n/a	chr6:25137823-25137831 chr6:25139267-25139275
36	STAT5A	chr6:25138120-25138856	GM12878	blood:	n/a	chr6:25138559-25138566
37	POLR2A	chr6:25137736-25139099	GM19193	blood:	n/a	n/a
38	BCLAF1	chr6:25138131-25139253	GM12878	blood:	n/a	chr6:25139184-25139193
39	POLR2A	chr6:25137724-25139403	GM18505	blood:	n/a	n/a
40	MXI1	chr6:25138097-25139225	GM12878	blood:	n/a	n/a
41	NFIC	chr6:25137972-25139433	GM12878	blood:	n/a	n/a
42	CEBPB	chr6:25137797-25138153	A549	lung:	n/a	n/a
43	MAX	chr6:25137797-25139372	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:25136994-25139133	GM19099	blood:	n/a	n/a
45	MEF2A	chr6:25138107-25139518	GM12878	blood:	n/a	chr6:25139225-25139239 chr6:25138248-25138263 chr6:25139092-25139109 chr6:25138248-25138265
46	RUNX3	chr6:25138117-25139453	GM12878	blood:	n/a	n/a
47	EP300	chr6:25137815-25139397	GM12878	blood:	n/a	chr6:25139184-25139198
48	POLR2A	chr6:25138153-25139142	GM15510	blood:	n/a	n/a
49	RELA	chr6:25137882-25139323	GM18951	blood:	n/a	n/a
50	POLR2A	chr6:25137754-25139347	GM12878	blood:	n/a	n/a

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

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs55851821	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs59778363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923293	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73386299	0.90[EUR][1000 genomes];0.92[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57003751	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25123800-25138400	Weak transcription	Pancreas	Pancrea
2	chr6:25124400-25138200	Weak transcription	Spleen	Spleen
3	chr6:25135200-25140200	Active TSS	Right Atrium	heart
4	chr6:25135400-25138200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:25136000-25138800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr6:25136000-25139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:25136200-25139000	Active TSS	Left Ventricle	heart
8	chr6:25136200-25139600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr6:25136200-25139800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr6:25136200-25140000	Active TSS	Aorta	Aorta
11	chr6:25136400-25138200	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr6:25136400-25139200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr6:25136400-25139400	Active TSS	Brain Hippocampus Middle	brain
14	chr6:25136600-25139400	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:25136600-25139600	Active TSS	Duodenum Mucosa	Duodenum
16	chr6:25136600-25140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:25136800-25138200	Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr6:25136800-25138400	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr6:25136800-25138400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr6:25136800-25138800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:25136800-25138800	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr6:25136800-25139000	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr6:25136800-25139000	Flanking Active TSS	Liver	Liver
24	chr6:25136800-25139000	Flanking Active TSS	Osteobl	bone
25	chr6:25136800-25139400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr6:25136800-25139400	Active TSS	Brain Anterior Caudate	brain
27	chr6:25136800-25139400	Active TSS	Right Ventricle	heart
28	chr6:25136800-25140000	Active TSS	Ovary	ovary
29	chr6:25137000-25138200	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr6:25137000-25138200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr6:25137000-25138200	Enhancers	Fetal Muscle Leg	muscle
32	chr6:25137000-25138200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
33	chr6:25137000-25138400	Enhancers	Fetal Stomach	stomach
34	chr6:25137000-25139000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:25137000-25139400	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr6:25137000-25139400	Active TSS	Colonic Mucosa	Colon
37	chr6:25137000-25139400	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr6:25137000-25139800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:25137000-25140200	Active TSS	Psoas Muscle	Psoas
40	chr6:25137200-25139600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:25137200-25139600	Active TSS	Rectal Smooth Muscle	rectum
42	chr6:25137400-25139400	Active TSS	Primary T cells fromperipheralblood	blood
43	chr6:25137400-25139400	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr6:25137400-25139400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr6:25137400-25139400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr6:25137400-25139400	Active TSS	Colon Smooth Muscle	Colon
47	chr6:25137400-25139400	Active TSS	GM12878-XiMat	blood
48	chr6:25137400-25139600	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr6:25137600-25138200	Weak transcription	Lung	lung
50	chr6:25137600-25138400	Active TSS	Small Intestine	intestine

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