Variant report

Variant	rs12639878
Chromosome Location	chr4:55809301-55809302
allele	A/C
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	chr4:55809267-55809416	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000248317	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10014134	0.95[EUR][1000 genomes]
rs11133349	0.81[EUR][1000 genomes]
rs1119545	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11721408	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11722896	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11732768	0.81[EUR][1000 genomes]
rs12639867	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643767	0.97[EUR][1000 genomes]
rs12646789	0.97[EUR][1000 genomes]
rs12646878	0.97[EUR][1000 genomes]
rs12647496	0.97[EUR][1000 genomes]
rs12648485	0.97[EUR][1000 genomes]
rs12648946	0.97[EUR][1000 genomes]
rs12649626	0.95[EUR][1000 genomes]
rs1497480	0.83[EUR][1000 genomes]
rs17084965	1.00[AFR][1000 genomes]
rs17085031	0.83[EUR][1000 genomes]
rs17085085	0.83[EUR][1000 genomes]
rs1874651	1.00[AFR][1000 genomes]
rs2088401	0.83[EUR][1000 genomes]
rs28435700	0.83[EUR][1000 genomes]
rs56288580	0.97[EUR][1000 genomes]
rs57491061	0.97[EUR][1000 genomes]
rs59049699	0.97[EUR][1000 genomes]
rs59527347	0.95[EUR][1000 genomes]
rs60317592	0.97[EUR][1000 genomes]
rs66857866	0.97[EUR][1000 genomes]
rs67682137	0.97[EUR][1000 genomes]
rs6833710	0.83[EUR][1000 genomes]
rs6851808	0.81[EUR][1000 genomes]
rs73143580	0.97[EUR][1000 genomes]
rs73234252	1.00[AFR][1000 genomes]
rs73234255	1.00[AFR][1000 genomes]
rs73234258	1.00[AFR][1000 genomes]
rs73234262	1.00[AFR][1000 genomes]
rs73234264	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73234265	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73234268	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73234269	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73234271	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73234272	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73234273	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73234275	0.93[EUR][1000 genomes]
rs73234276	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73234277	0.97[EUR][1000 genomes]
rs73234278	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7682627	0.81[EUR][1000 genomes]
rs904130	0.83[EUR][1000 genomes]
rs904132	0.95[EUR][1000 genomes]
rs904133	0.95[EUR][1000 genomes]
rs969341	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv948758	chr4:55748430-55887962	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3366988	chr4:55808045-55809893	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2521332	chr4:55808162-55809636	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55796800-55810200	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:55804200-55811200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:55806000-55809600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:55806000-55809800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:55806200-55810000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr4:55806400-55809600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:55806800-55809600	Enhancers	Primary B cells from peripheral blood	blood
8	chr4:55806800-55812600	Enhancers	Fetal Thymus	thymus
9	chr4:55807200-55810400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:55808200-55812600	Enhancers	HUVEC	blood vessel
11	chr4:55808400-55810000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr4:55808400-55812000	Weak transcription	Adipose Nuclei	Adipose
13	chr4:55808400-55812600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr4:55808400-55812600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr4:55808600-55809800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr4:55808600-55811000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:55808600-55813000	Enhancers	Primary T cells from cord blood	blood
18	chr4:55809000-55809400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:55809000-55809400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:55809000-55809800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:55809000-55810400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr4:55809200-55809400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:55809200-55809400	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr4:55809200-55809600	Enhancers	Primary B cells from cord blood	blood
25	chr4:55809200-55809600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr4:55809200-55809800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr4:55809200-55809800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr4:55809200-55810800	Weak transcription	Fetal Stomach	stomach
29	chr4:55809200-55811800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:55809200-55812600	Enhancers	Primary hematopoietic stem cells	blood
31	chr4:55809200-55814000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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