Variant report

Variant	rs28688534
Chromosome Location	chr7:138238898-138238899
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	chr7:138233620-138239073	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:138237455-138238949	K562	blood:	n/a	n/a
3	POLR2A	chr7:138238617-138239052	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:138238462-138238976	HepG2	liver:	n/a	n/a
5	POLR2A	chr7:138238600-138238985	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr7:138238452-138239012	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr7:138236657-138239082	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:138236458..138239025-chr7:138241233..138243076,2	K562	blood:

Variant related genes	Relation type
TRIM24	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10224063	1.00[AMR][1000 genomes]
rs10224459	0.89[AFR][1000 genomes]
rs10224559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10226487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10227148	1.00[AMR][1000 genomes]
rs10229259	1.00[AMR][1000 genomes]
rs10229430	1.00[AMR][1000 genomes]
rs10231698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10232500	1.00[AMR][1000 genomes]
rs10232597	0.88[AFR][1000 genomes]
rs10234810	0.91[AFR][1000 genomes]
rs10236859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10237069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10237544	0.91[AFR][1000 genomes]
rs10237720	0.94[AFR][1000 genomes]
rs10239129	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10239202	0.94[AFR][1000 genomes]
rs10239932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10240387	1.00[AMR][1000 genomes]
rs10241288	0.91[AFR][1000 genomes]
rs10241942	0.94[AFR][1000 genomes]
rs10242105	0.94[AFR][1000 genomes]
rs10243069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10245088	0.94[AFR][1000 genomes]
rs10248027	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10248255	1.00[AMR][1000 genomes]
rs10248604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10249171	1.00[AMR][1000 genomes]
rs10253989	0.80[AFR][1000 genomes]
rs10254196	1.00[AMR][1000 genomes]
rs10254440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10254935	0.85[AFR][1000 genomes]
rs10256094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10256358	0.94[AFR][1000 genomes]
rs10256619	0.88[AFR][1000 genomes]
rs10256953	1.00[AMR][1000 genomes]
rs10258403	1.00[AMR][1000 genomes]
rs10259673	0.94[AFR][1000 genomes]
rs10261219	1.00[AMR][1000 genomes]
rs10261236	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10262919	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10267577	0.94[AFR][1000 genomes]
rs10268912	0.94[AFR][1000 genomes]
rs10272478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10274764	1.00[AMR][1000 genomes]
rs10277465	0.94[AFR][1000 genomes]
rs10278741	0.94[AFR][1000 genomes]
rs10281429	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10281487	0.94[AFR][1000 genomes]
rs1073255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11506000	1.00[AMR][1000 genomes]
rs11983193	1.00[AMR][1000 genomes]
rs13438570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28361932	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28380017	0.89[AFR][1000 genomes]
rs28392567	0.91[AFR][1000 genomes]
rs28407067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28435503	1.00[AMR][1000 genomes]
rs28480333	1.00[AMR][1000 genomes]
rs28498774	0.91[AFR][1000 genomes]
rs28502705	0.94[AFR][1000 genomes]
rs28514575	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28534820	0.94[AFR][1000 genomes]
rs28546247	1.00[AMR][1000 genomes]
rs28584756	0.94[AFR][1000 genomes]
rs28593099	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28598597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28608602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28653145	1.00[AMR][1000 genomes]
rs28673291	0.91[AFR][1000 genomes]
rs28691741	1.00[AMR][1000 genomes]
rs28694658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28707292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28714460	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28729263	0.91[AFR][1000 genomes]
rs28762120	0.85[AFR][1000 genomes]
rs28764878	0.91[AFR][1000 genomes]
rs28816768	0.91[AFR][1000 genomes]
rs28822161	0.88[AFR][1000 genomes]
rs28824911	1.00[AMR][1000 genomes]
rs28850964	1.00[AMR][1000 genomes]
rs3847123	0.94[AFR][1000 genomes]
rs3847124	0.94[AFR][1000 genomes]
rs4329204	0.88[AFR][1000 genomes]
rs9986844	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831153	chr7:138078179-138265648	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138213000-138239400	Weak transcription	Right Atrium	heart
2	chr7:138213000-138244200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:138220200-138240400	Weak transcription	Psoas Muscle	Psoas
4	chr7:138221200-138241400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:138222200-138239400	Strong transcription	Fetal Thymus	thymus
6	chr7:138222400-138239400	Strong transcription	K562	blood
7	chr7:138224400-138239400	Weak transcription	Stomach Mucosa	stomach
8	chr7:138225400-138242000	Weak transcription	A549	lung
9	chr7:138227000-138241200	Weak transcription	Hela-S3	cervix
10	chr7:138228400-138239800	Strong transcription	Fetal Lung	lung
11	chr7:138228400-138252600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:138228600-138239400	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:138229200-138239400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:138231200-138240600	Weak transcription	NHLF	lung
15	chr7:138232200-138241600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr7:138232600-138241600	Strong transcription	HepG2	liver
17	chr7:138232800-138239600	Strong transcription	Fetal Intestine Large	intestine
18	chr7:138233800-138239400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr7:138233800-138240400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr7:138233800-138240400	Strong transcription	Fetal Heart	heart
21	chr7:138234000-138239600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr7:138234400-138240600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr7:138234600-138240600	Weak transcription	NHEK	skin
24	chr7:138234600-138243600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
25	chr7:138234800-138241000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:138234800-138241400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:138235000-138240600	Strong transcription	HUVEC	blood vessel
28	chr7:138235000-138248600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:138235000-138257400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:138235200-138239400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:138235200-138240000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr7:138235200-138240600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:138235200-138240800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:138235200-138241200	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:138235200-138241200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr7:138235200-138241600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:138235400-138241400	Strong transcription	Liver	Liver
38	chr7:138235600-138239000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:138235600-138239200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:138235600-138239600	Strong transcription	Colonic Mucosa	Colon
41	chr7:138235600-138240600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:138235600-138241400	Strong transcription	Brain Hippocampus Middle	brain
43	chr7:138235600-138245200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:138235800-138239600	Strong transcription	Fetal Brain Female	brain
45	chr7:138235800-138239600	Strong transcription	Osteobl	bone
46	chr7:138235800-138239800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
47	chr7:138235800-138240000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:138235800-138240600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:138235800-138240600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr7:138235800-138240600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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