Variant report

Variant	rs73831565
Chromosome Location	chr3:48340082-48340083
allele	C/T
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	chr3:48339592-48340104	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:48340005-48340174	K562	blood:	n/a	n/a
3	POLR2A	chr3:48339927-48340149	K562	blood:	n/a	n/a
4	POLR2A	chr3:48339801-48340129	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48335073..48340448-chr3:48341483..48344077,7	K562	blood:
2	chr3:48328476..48331026-chr3:48338311..48340193,2	MCF-7	breast:

Variant related genes	Relation type
NME6	TF binding region
ENSG00000199476	Chromatin interaction
ENSG00000172113	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10780032	1.00[EUR][1000 genomes]
rs11130169	1.00[EUR][1000 genomes]
rs11915428	1.00[EUR][1000 genomes]
rs34146962	0.82[AFR][1000 genomes]
rs35703936	0.80[AFR][1000 genomes]
rs3731495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3731539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3731547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3924179	1.00[EUR][1000 genomes]
rs4476528	1.00[AMR][1000 genomes]
rs4858818	1.00[EUR][1000 genomes]
rs55782175	1.00[EUR][1000 genomes]
rs6442103	1.00[EUR][1000 genomes]
rs6442104	1.00[AMR][1000 genomes]
rs6442122	1.00[EUR][1000 genomes]
rs6773945	1.00[AMR][1000 genomes]
rs6793732	1.00[EUR][1000 genomes]
rs6801348	1.00[EUR][1000 genomes]
rs7372108	1.00[AMR][1000 genomes]
rs73831562	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];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]
rs9863220	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917799	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48329200-48341400	Weak transcription	Small Intestine	intestine
2	chr3:48330400-48340200	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr3:48330800-48340200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:48331600-48341200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:48332000-48340400	Strong transcription	Primary B cells from cord blood	blood
6	chr3:48332400-48340200	Strong transcription	Primary T cells from cord blood	blood
7	chr3:48332400-48340200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr3:48332400-48340800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:48332600-48340200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:48333400-48340400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:48333600-48340200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:48333600-48340200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr3:48333600-48340200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:48333600-48340200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:48333600-48340600	Strong transcription	Fetal Brain Female	brain
16	chr3:48333800-48340200	Strong transcription	Fetal Thymus	thymus
17	chr3:48333800-48340400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:48333800-48340600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:48334000-48340200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:48334000-48340200	Strong transcription	Fetal Stomach	stomach
21	chr3:48334000-48340400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:48334000-48340400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:48334200-48340200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:48334200-48340200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr3:48334200-48340200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:48334200-48340200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:48334200-48340200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:48334200-48340200	Strong transcription	Ovary	ovary
29	chr3:48334200-48340400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:48334200-48340800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:48334400-48340200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:48334400-48340200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:48334400-48340200	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr3:48334400-48340200	Strong transcription	Colonic Mucosa	Colon
35	chr3:48334400-48340200	Strong transcription	Osteobl	bone
36	chr3:48334400-48340400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr3:48334400-48340600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:48334400-48341000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:48334400-48341400	Strong transcription	HSMM	muscle
40	chr3:48334600-48340200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:48334800-48341400	Weak transcription	Right Atrium	heart
42	chr3:48335400-48341400	Weak transcription	Stomach Mucosa	stomach
43	chr3:48335800-48340200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:48335800-48340200	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr3:48336800-48340600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:48336800-48341800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:48337000-48341800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:48337200-48341200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:48337200-48341200	Strong transcription	K562	blood
50	chr3:48338200-48340200	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links