Variant report

Variant	rs6762888
Chromosome Location	chr3:48557639-48557640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48549854..48552733-chr3:48556250..48558501,2	MCF-7	breast:
2	chr3:48553221..48555693-chr3:48556797..48558474,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11915428	0.95[AFR][1000 genomes]
rs3924179	1.00[AFR][1000 genomes]
rs55782175	0.92[AFR][1000 genomes]
rs6442122	0.93[YRI][hapmap]
rs6787988	0.81[YRI][hapmap]
rs73831579	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs876597	0.82[ASW][hapmap]
rs898226	0.90[AFR][1000 genomes]
rs9852211	1.00[ASW][hapmap]
rs986742	0.82[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48542800-48558200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:48542800-48562800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:48542800-48569800	Weak transcription	Right Atrium	heart
4	chr3:48544000-48561000	Weak transcription	K562	blood
5	chr3:48545000-48559800	Weak transcription	Fetal Intestine Large	intestine
6	chr3:48545200-48558400	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:48545200-48558600	Weak transcription	NHLF	lung
8	chr3:48545200-48572400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:48545400-48558400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:48545400-48558800	Weak transcription	Gastric	stomach
11	chr3:48545400-48565400	Weak transcription	Pancreas	Pancrea
12	chr3:48545400-48572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:48545400-48572600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:48545600-48562600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:48545600-48570600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:48545600-48571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:48545600-48572600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:48547400-48559000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:48547400-48562000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:48550400-48557800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr3:48551600-48558200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:48552600-48558000	Enhancers	Primary T cells fromperipheralblood	blood
24	chr3:48552800-48572600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:48553200-48558400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:48553400-48558400	Weak transcription	A549	lung
27	chr3:48553600-48559400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:48553600-48564000	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:48554000-48573000	Weak transcription	Right Ventricle	heart
30	chr3:48554200-48557800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:48554200-48557800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr3:48554200-48559600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:48554200-48561000	Weak transcription	Lung	lung
34	chr3:48554200-48565000	Strong transcription	Fetal Intestine Small	intestine
35	chr3:48554200-48572600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:48554200-48572600	Weak transcription	Dnd41	blood
37	chr3:48554400-48557800	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:48554400-48558000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:48554400-48561200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:48554400-48562600	Weak transcription	NHEK	skin
41	chr3:48554400-48572600	Weak transcription	Aorta	Aorta
42	chr3:48554600-48562200	Weak transcription	Ovary	ovary
43	chr3:48554800-48558800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:48554800-48563400	Strong transcription	Brain Germinal Matrix	brain
45	chr3:48554800-48566400	Strong transcription	Fetal Brain Female	brain
46	chr3:48554800-48570800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr3:48555000-48563000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:48555200-48582200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:48555400-48565800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:48555400-48572600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links