Variant report

Variant	rs58814661
Chromosome Location	chr3:61622344-61622345
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:56734753..56737927-chr3:61621064..61623984,6	MCF-7	breast:
2	chr17:56734576..56737757-chr3:61620422..61625373,6	MCF-7	breast:
3	chr3:61621266..61623039-chr3:61662503..61664613,2	MCF-7	breast:
4	chr3:61620655..61625316-chr3:61640653..61644936,5	MCF-7	breast:
5	chr17:56704810..56711827-chr3:61617461..61633126,28	MCF-7	breast:
6	chr17:56703125..56711935-chr3:61611656..61626888,27	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs4390920	1.00[AMR][1000 genomes]
rs56696131	1.00[AMR][1000 genomes]
rs57943064	1.00[AMR][1000 genomes]
rs57953857	1.00[AMR][1000 genomes]
rs60197600	1.00[AMR][1000 genomes]
rs60197976	1.00[AMR][1000 genomes]
rs60473152	1.00[AMR][1000 genomes]
rs6801604	1.00[AMR][1000 genomes]
rs6805288	1.00[AMR][1000 genomes]
rs72874738	1.00[AMR][1000 genomes]
rs72874741	1.00[AMR][1000 genomes]
rs72874744	1.00[AMR][1000 genomes]
rs72874746	1.00[AMR][1000 genomes]
rs72874749	1.00[AMR][1000 genomes]
rs72874755	1.00[AMR][1000 genomes]
rs72888670	1.00[AMR][1000 genomes]
rs72888675	1.00[AMR][1000 genomes]
rs72888676	1.00[AMR][1000 genomes]
rs72888678	1.00[AMR][1000 genomes]
rs7640772	1.00[AMR][1000 genomes]
rs9878929	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2756995	chr3:61569557-61636156	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv2759153	chr3:61569557-61636156	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	esv35004	chr3:61570149-61626426	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv822106	chr3:61577755-61631078	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv1001611	chr3:61598148-61686809	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1000158	chr3:61598562-61682888	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv834712	chr3:61612540-61770232	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61598800-61623200	Weak transcription	Aorta	Aorta
2	chr3:61603200-61623400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:61603400-61622600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:61603600-61622800	Weak transcription	Ovary	ovary
5	chr3:61612000-61625600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:61612600-61623000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:61612600-61623200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:61613600-61622600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:61613800-61622400	Weak transcription	Fetal Intestine Large	intestine
10	chr3:61613800-61623200	Weak transcription	HUVEC	blood vessel
11	chr3:61613800-61625000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:61615800-61622600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:61615800-61625800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:61616000-61633800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:61616200-61623000	Weak transcription	NH-A	brain
16	chr3:61616400-61630200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:61616800-61622800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:61616800-61633600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:61618600-61622600	Weak transcription	NHLF	lung
20	chr3:61618600-61623000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:61618800-61622800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:61618800-61624800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:61619000-61623000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:61619000-61623000	Weak transcription	HSMM	muscle
25	chr3:61619000-61626000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:61619200-61623000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:61619200-61628000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:61619200-61630000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:61619400-61623200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:61620000-61622600	Enhancers	Fetal Heart	heart
31	chr3:61620200-61623000	Weak transcription	Psoas Muscle	Psoas
32	chr3:61620400-61623000	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:61620600-61622600	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:61620600-61622800	Weak transcription	NHDF-Ad	bronchial
35	chr3:61620600-61623000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:61620600-61630200	Weak transcription	Fetal Kidney	kidney
37	chr3:61620800-61622400	Weak transcription	Fetal Intestine Small	intestine
38	chr3:61620800-61622400	Weak transcription	HepG2	liver
39	chr3:61620800-61622600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:61620800-61622600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:61620800-61622800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:61620800-61622800	Weak transcription	Fetal Lung	lung
43	chr3:61620800-61622800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:61620800-61623000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:61620800-61623000	Weak transcription	Osteobl	bone
46	chr3:61620800-61623200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:61620800-61623200	Weak transcription	Right Ventricle	heart
48	chr3:61620800-61623200	Weak transcription	HSMMtube	muscle
49	chr3:61620800-61625800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:61620800-61625800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links