Variant report

Variant	rs1979972
Chromosome Location	chr4:48138613-48138614
allele	A/G
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	chr4:48136964-48138816	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:48137561-48138741	GM12891	blood:	n/a	n/a
3	POLR2A	chr4:48137788-48138663	GM12892	blood:	n/a	n/a
4	POLR2A	chr4:48137622-48138647	GM12892	blood:	n/a	n/a
5	POLR2A	chr4:48137727-48138638	GM12891	blood:	n/a	n/a
6	POLR2A	chr4:48137778-48141212	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TXK	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1396049	0.83[AMR][1000 genomes]
rs1507923	1.00[YRI][hapmap]
rs16860943	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16861067	1.00[AMR][1000 genomes]
rs2089508	1.00[AMR][1000 genomes]
rs2135957	0.83[AMR][1000 genomes]
rs2251240	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2352590	0.83[AMR][1000 genomes]
rs2352591	0.83[AMR][1000 genomes]
rs2456926	0.83[AMR][1000 genomes]
rs2464500	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2464501	0.83[AMR][1000 genomes]
rs2464506	0.83[AMR][1000 genomes]
rs2661526	1.00[AMR][1000 genomes]
rs2661527	1.00[AMR][1000 genomes]
rs2661531	1.00[AMR][1000 genomes]
rs2661534	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2704397	1.00[AMR][1000 genomes]
rs2704398	1.00[AMR][1000 genomes]
rs2704427	1.00[AMR][1000 genomes]
rs2704428	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2704429	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2704432	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2940329	1.00[AMR][1000 genomes]
rs34386002	1.00[AMR][1000 genomes]
rs3857073	0.83[AMR][1000 genomes]
rs4695333	0.83[AMR][1000 genomes]
rs60470389	1.00[AMR][1000 genomes]
rs6830656	1.00[YRI][hapmap]
rs6832090	1.00[YRI][hapmap]
rs6858033	0.83[AMR][1000 genomes]
rs7692882	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48129800-48140800	Weak transcription	Fetal Stomach	stomach
2	chr4:48129800-48157400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:48130400-48139000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:48130400-48139800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:48130400-48152200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:48130400-48155400	Weak transcription	Psoas Muscle	Psoas
7	chr4:48130400-48156200	Weak transcription	Adipose Nuclei	Adipose
8	chr4:48130400-48156800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:48130400-48157600	Weak transcription	Colonic Mucosa	Colon
10	chr4:48130600-48142800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:48130600-48146000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:48131800-48141400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:48131800-48142000	Weak transcription	NHLF	lung
14	chr4:48132000-48141400	Weak transcription	HUVEC	blood vessel
15	chr4:48132000-48141600	Weak transcription	NHDF-Ad	bronchial
16	chr4:48132000-48157000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:48132000-48157200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:48132200-48138800	Weak transcription	Stomach Mucosa	stomach
19	chr4:48132200-48139800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:48132200-48141800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:48132400-48142000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:48132600-48140200	Weak transcription	Right Ventricle	heart
23	chr4:48132600-48141000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:48133000-48141800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:48133000-48151400	Weak transcription	HSMMtube	muscle
26	chr4:48133000-48153000	Weak transcription	Placenta	Placenta
27	chr4:48133200-48140400	Weak transcription	Left Ventricle	heart
28	chr4:48133200-48141000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:48133200-48141800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:48134600-48140600	Weak transcription	Fetal Kidney	kidney
31	chr4:48134800-48141400	Weak transcription	Fetal Brain Male	brain
32	chr4:48135400-48140400	Strong transcription	GM12878-XiMat	blood
33	chr4:48135400-48142200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:48135600-48142800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr4:48136000-48140400	Weak transcription	Small Intestine	intestine
36	chr4:48136000-48140600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:48136000-48141000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr4:48136200-48139400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr4:48136400-48139800	Strong transcription	Primary hematopoietic stem cells	blood
40	chr4:48136400-48139800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:48136400-48141200	Strong transcription	K562	blood
42	chr4:48136600-48139000	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr4:48136600-48139000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:48136600-48139800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr4:48136600-48139800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:48136800-48139000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr4:48136800-48139400	Strong transcription	Primary B cells from cord blood	blood
48	chr4:48136800-48139600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr4:48136800-48139800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:48136800-48140600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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