Variant report

Variant	rs6925139
Chromosome Location	chr6:144288284-144288285
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	TBP	chr6:144288028-144288346	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr6:144288155-144288406	IMR90	lung:	n/a	n/a
3	CEBPB	chr6:144288203-144288462	H1-hESC	embryonic stem cell:	n/a	n/a
4	TBP	chr6:144288068-144288297	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:144286646..144289265-chr6:144304089..144305699,2	K562	blood:
2	chr6:143832151..143834228-chr6:144285681..144288374,2	MCF-7	breast:
3	chr6:144286109..144288326-chr6:144291907..144294386,3	K562	blood:

Variant related genes	Relation type
PLAGL1	TF binding region
ENSG00000001036	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11961603	1.00[EUR][1000 genomes]
rs11964079	1.00[MEX][hapmap]
rs2010247	1.00[EUR][1000 genomes]
rs57960633	1.00[EUR][1000 genomes]
rs59407195	1.00[EUR][1000 genomes]
rs6902313	1.00[MEX][hapmap]
rs6909239	1.00[EUR][1000 genomes]
rs6910132	1.00[AMR][1000 genomes]
rs6912793	1.00[MEX][hapmap]
rs6914895	1.00[MEX][hapmap]
rs6917779	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7740089	1.00[TSI][hapmap]
rs7743408	1.00[EUR][1000 genomes]
rs7744101	1.00[MEX][hapmap]
rs7768171	1.00[EUR][1000 genomes]
rs7773115	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9484844	1.00[EUR][1000 genomes]
rs9496885	1.00[TSI][hapmap]

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	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3522138	chr6:144174685-144367463	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3522139	chr6:144174685-144367463	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830830	chr6:144177942-144380870	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6925139	LOC285740	cis	lymphoblastoid	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144269200-144290200	Weak transcription	Fetal Thymus	thymus
2	chr6:144269400-144289600	Weak transcription	Pancreas	Pancrea
3	chr6:144269600-144294000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:144269800-144289800	Weak transcription	Ovary	ovary
5	chr6:144269800-144296000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:144269800-144304400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:144271400-144296800	Weak transcription	Primary B cells from cord blood	blood
8	chr6:144274400-144289800	Weak transcription	Esophagus	oesophagus
9	chr6:144275000-144293000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:144277200-144291200	Genic enhancers	Fetal Muscle Leg	muscle
11	chr6:144280200-144290400	Weak transcription	Fetal Heart	heart
12	chr6:144280400-144291400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:144281800-144294800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:144284200-144289000	Weak transcription	NHLF	lung
15	chr6:144284600-144288400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr6:144284600-144290600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:144284800-144294400	Weak transcription	Fetal Brain Male	brain
18	chr6:144284800-144318400	Weak transcription	Aorta	Aorta
19	chr6:144285000-144292400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:144285200-144288400	Strong transcription	Primary hematopoietic stem cells	blood
21	chr6:144285200-144289000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:144285400-144291400	Weak transcription	Colonic Mucosa	Colon
23	chr6:144285400-144294200	Weak transcription	Left Ventricle	heart
24	chr6:144285800-144293400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:144286000-144288400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:144286000-144290400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr6:144286200-144289800	Weak transcription	Right Atrium	heart
28	chr6:144286400-144288400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:144286400-144288600	Genic enhancers	Placenta	Placenta
30	chr6:144286600-144290000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:144286800-144289000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:144286800-144290400	Strong transcription	Fetal Intestine Large	intestine
33	chr6:144286800-144294200	Weak transcription	Fetal Brain Female	brain
34	chr6:144287000-144289200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:144287000-144290600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr6:144287000-144293000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:144287000-144294400	Weak transcription	Lung	lung
38	chr6:144287000-144294800	Weak transcription	Spleen	Spleen
39	chr6:144287000-144298800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:144287200-144288800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:144287200-144290800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:144287200-144293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:144287200-144293200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:144287200-144293400	Weak transcription	Fetal Intestine Small	intestine
45	chr6:144287400-144288800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:144287400-144288800	Weak transcription	Fetal Stomach	stomach
47	chr6:144287400-144289800	Weak transcription	GM12878-XiMat	blood
48	chr6:144287400-144289800	Weak transcription	K562	blood
49	chr6:144287400-144291000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:144287400-144294600	Enhancers	Adipose Nuclei	Adipose

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