Variant report

Variant	rs509729
Chromosome Location	chr13:30688459-30688460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:30421278..30427133-chr13:30682148..30691157,22	MCF-7	breast:
2	chr13:30407057..30408678-chr13:30687938..30689811,2	MCF-7	breast:
3	chr13:30344222..30347052-chr13:30686907..30688799,2	MCF-7	breast:
4	chr13:30681624..30684735-chr13:30687394..30690983,4	MCF-7	breast:
5	chr13:30422658..30425963-chr13:30681369..30690318,16	MCF-7	breast:
6	chr13:30687700..30689739-chr13:30690747..30693968,3	MCF-7	breast:
7	chr13:30403000..30404793-chr13:30686519..30690620,3	MCF-7	breast:
8	chr13:30687723..30690408-chr13:30699734..30701487,2	MCF-7	breast:
9	chr13:30494996..30500904-chr13:30681667..30688775,12	MCF-7	breast:
10	chr13:30651986..30653783-chr13:30687863..30690496,2	MCF-7	breast:
11	chr13:30687670..30690211-chr13:30694014..30695972,2	MCF-7	breast:
12	chr13:30680284..30681903-chr13:30686575..30689356,2	K562	blood:
13	chr13:30687972..30690132-chr13:31190210..31193033,2	MCF-7	breast:
14	chr13:30268179..30269731-chr13:30686906..30689381,2	MCF-7	breast:
15	chr13:30687032..30689624-chr13:30701987..30704608,2	MCF-7	breast:
16	chr13:30618914..30621589-chr13:30687239..30690336,3	MCF-7	breast:
17	chr13:30342827..30348055-chr13:30683488..30688791,7	MCF-7	breast:
18	chr13:30415961..30419397-chr13:30686617..30690558,4	MCF-7	breast:
19	chr13:30347146..30349526-chr13:30687739..30689607,2	MCF-7	breast:
20	chr13:30416529..30418789-chr13:30687600..30690547,3	MCF-7	breast:
21	chr13:30495539..30501420-chr13:30683250..30690010,13	MCF-7	breast:
22	chr13:30686343..30690173-chr13:31036596..31040141,3	MCF-7	breast:
23	chr13:30418877..30421858-chr13:30687750..30689569,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000132952	Chromatin interaction
ENSG00000224405	Chromatin interaction
ENSG00000122042	Chromatin interaction
ENSG00000189403	Chromatin interaction
ENSG00000224511	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs472160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs501877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs501911	1.00[AMR][1000 genomes]
rs506517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs537597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56292131	1.00[AMR][1000 genomes]
rs564949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58426783	1.00[AFR][1000 genomes]
rs58662887	1.00[AMR][1000 genomes]
rs602584	1.00[AFR][1000 genomes]
rs60673071	1.00[AMR][1000 genomes]
rs631673	1.00[AMR][1000 genomes]
rs658913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs663161	1.00[AMR][1000 genomes]
rs683993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74043017	1.00[AMR][1000 genomes]
rs74043029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74043032	1.00[AFR][1000 genomes]
rs74043047	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040215	chr13:30621351-30741022	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541745	chr13:30621351-30741022	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30682800-30688600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:30683400-30688800	Weak transcription	Lung	lung
3	chr13:30683600-30688800	Weak transcription	Esophagus	oesophagus
4	chr13:30683800-30688600	Weak transcription	Right Atrium	heart
5	chr13:30686600-30688600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:30686800-30688600	Enhancers	Primary B cells from peripheral blood	blood
7	chr13:30686800-30688600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr13:30686800-30688600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr13:30686800-30688600	Enhancers	Adipose Nuclei	Adipose
10	chr13:30686800-30688600	Enhancers	Colon Smooth Muscle	Colon
11	chr13:30686800-30688600	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr13:30686800-30688800	Flanking Active TSS	HepG2	liver
13	chr13:30687000-30688800	Weak transcription	Gastric	stomach
14	chr13:30687000-30688800	Enhancers	K562	blood
15	chr13:30687200-30688600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:30687200-30688600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr13:30687200-30688600	Weak transcription	Primary B cells from cord blood	blood
18	chr13:30687200-30688600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr13:30687200-30688600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr13:30687200-30688600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:30687200-30688600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr13:30687200-30688600	Enhancers	Brain Cingulate Gyrus	brain
23	chr13:30687200-30688600	Enhancers	Brain Substantia Nigra	brain
24	chr13:30687200-30688600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr13:30687200-30688600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:30687200-30688600	Enhancers	HMEC	breast
27	chr13:30687200-30688600	Enhancers	NHDF-Ad	bronchial
28	chr13:30687200-30688600	Weak transcription	NHLF	lung
29	chr13:30687200-30688800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr13:30687400-30688600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:30687400-30688600	Enhancers	Brain Angular Gyrus	brain
32	chr13:30687400-30688600	Enhancers	Osteobl	bone
33	chr13:30687400-30689000	Weak transcription	Fetal Kidney	kidney
34	chr13:30687600-30688600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr13:30687600-30688600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:30687600-30688600	Weak transcription	Fetal Brain Male	brain
37	chr13:30687600-30688600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr13:30687600-30688600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr13:30687600-30688800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr13:30687600-30689200	Weak transcription	Fetal Lung	lung
41	chr13:30687600-30689800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:30687800-30688600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:30687800-30688800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr13:30687800-30688800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr13:30687800-30688800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr13:30687800-30688800	Enhancers	Small Intestine	intestine
47	chr13:30687800-30689400	Enhancers	Placenta	Placenta
48	chr13:30688000-30688600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr13:30688000-30688600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
50	chr13:30688000-30688600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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