Variant report

Variant	rs59352296
Chromosome Location	chr3:48645936-48645937
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	chr3:48645919-48645987	MCF10A-Er-Src	breast:	n/a	n/a
2	ESRRA	chr3:48645659-48647537	GM12878	blood:	n/a	chr3:48646221-48646233 chr3:48646514-48646526 chr3:48646858-48646871 chr3:48646221-48646231 chr3:48646864-48646882 chr3:48646220-48646233 chr3:48646860-48646870 chr3:48646514-48646530 chr3:48646217-48646233 chr3:48646516-48646526 chr3:48646221-48646231 chr3:48646514-48646527

No.	Distal block	Cell Line	Cell type
1	chr3:48603540..48606248-chr3:48645461..48648473,3	K562	blood:
2	chr3:48645687..48647354-chr3:48671015..48673103,2	MCF-7	breast:
3	chr3:48338306..48341103-chr3:48643663..48646394,2	K562	blood:
4	chr3:48637965..48640004-chr3:48645401..48647013,2	MCF-7	breast:
5	chr3:48639116..48644270-chr3:48645185..48648761,6	K562	blood:
6	chr3:48644319..48649140-chr3:48667292..48673836,7	K562	blood:
7	chr3:48614996..48616945-chr3:48645477..48647232,2	K562	blood:
8	chr3:48637721..48640479-chr3:48645220..48647782,4	MCF-7	breast:
9	chr3:48643318..48645059-chr3:48645193..48646900,2	MCF-7	breast:
10	chr3:48640950..48644386-chr3:48644481..48647187,5	MCF-7	breast:
11	chr3:48604748..48607009-chr3:48645461..48648457,2	K562	blood:

Variant related genes	Relation type
UQCRC1	TF binding region
ENSG00000225697	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000211535	Chromatin interaction
ENSG00000172113	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10780032	1.00[EUR][1000 genomes]
rs11130169	1.00[EUR][1000 genomes]
rs11915428	1.00[EUR][1000 genomes]
rs13318132	1.00[EUR][1000 genomes]
rs14828	1.00[EUR][1000 genomes]
rs28523319	1.00[EUR][1000 genomes]
rs3924179	1.00[EUR][1000 genomes]
rs4858818	1.00[EUR][1000 genomes]
rs55782175	1.00[EUR][1000 genomes]
rs58708931	1.00[EUR][1000 genomes]
rs58835493	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58914641	1.00[EUR][1000 genomes]
rs60338814	1.00[EUR][1000 genomes]
rs60352528	1.00[EUR][1000 genomes]
rs6442122	1.00[EUR][1000 genomes]
rs6791777	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793732	1.00[EUR][1000 genomes]
rs6801348	1.00[EUR][1000 genomes]
rs72930094	1.00[EUR][1000 genomes]
rs72931155	1.00[EUR][1000 genomes]
rs72931157	1.00[EUR][1000 genomes]
rs72931171	1.00[EUR][1000 genomes]
rs73830466	1.00[EUR][1000 genomes]
rs73830478	1.00[EUR][1000 genomes]
rs73831572	1.00[EUR][1000 genomes]
rs73831577	1.00[EUR][1000 genomes]
rs73831579	1.00[EUR][1000 genomes]
rs7633433	1.00[EUR][1000 genomes]
rs898226	1.00[EUR][1000 genomes]
rs9852211	1.00[EUR][1000 genomes]
rs9860187	1.00[EUR][1000 genomes]
rs9876812	1.00[EUR][1000 genomes]
rs9882714	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 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	chr3:48634200-48646200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:48641600-48646000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:48642600-48646000	Weak transcription	Stomach Mucosa	stomach
4	chr3:48642800-48646000	Weak transcription	Fetal Brain Male	brain
5	chr3:48643200-48646200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:48643200-48646200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:48643400-48646200	Weak transcription	Esophagus	oesophagus
8	chr3:48643600-48646000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:48643600-48646000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:48643600-48646000	Weak transcription	Brain Substantia Nigra	brain
11	chr3:48643600-48646000	Weak transcription	Fetal Brain Female	brain
12	chr3:48643600-48646000	Weak transcription	Thymus	Thymus
13	chr3:48643600-48646200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:48643600-48646200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:48643600-48646200	Weak transcription	Aorta	Aorta
16	chr3:48643600-48646200	Weak transcription	Colonic Mucosa	Colon
17	chr3:48643600-48646200	Weak transcription	Gastric	stomach
18	chr3:48643600-48646200	Weak transcription	Lung	lung
19	chr3:48643600-48646200	Weak transcription	Ovary	ovary
20	chr3:48643600-48646200	Weak transcription	Pancreas	Pancrea
21	chr3:48643600-48646200	Weak transcription	HSMMtube	muscle
22	chr3:48644400-48646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:48644600-48646200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:48645000-48646000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:48645000-48646200	Enhancers	Primary T cells fromperipheralblood	blood
26	chr3:48645000-48646200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr3:48645000-48646200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:48645000-48646400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:48645200-48646000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr3:48645200-48646000	Genic enhancers	NHLF	lung
31	chr3:48645200-48647200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:48645400-48646000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:48645400-48646000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:48645400-48646000	Genic enhancers	Brain Angular Gyrus	brain
35	chr3:48645400-48646000	Genic enhancers	Fetal Intestine Small	intestine
36	chr3:48645400-48646000	Weak transcription	Placenta	Placenta
37	chr3:48645400-48646000	Weak transcription	Fetal Thymus	thymus
38	chr3:48645400-48646000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr3:48645400-48646000	Enhancers	Rectal Smooth Muscle	rectum
40	chr3:48645400-48646200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr3:48645400-48646200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:48645400-48646200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr3:48645400-48646200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:48645400-48646200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:48645400-48646200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr3:48645400-48646200	Enhancers	Fetal Lung	lung
47	chr3:48645600-48646000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:48645600-48646000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
49	chr3:48645600-48646000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
50	chr3:48645600-48646000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links