Variant report

Variant	rs2444961
Chromosome Location	chr15:33425360-33425361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:33136051..33136687-chr15:33424687..33425559,2	K562	blood:
2	chr15:33425198..33426849-chr15:33434224..33436145,2	K562	blood:
3	chr15:33378091..33379388-chr15:33424633..33425509,8	MCF-7	breast:
4	chr15:33357010..33360956-chr15:33425226..33427691,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17235701	0.86[JPT][hapmap]
rs17235722	0.86[JPT][hapmap]
rs1988447	0.86[JPT][hapmap]
rs3850097	0.86[JPT][hapmap]
rs3861200	0.86[JPT][hapmap]
rs8023846	0.87[LWK][hapmap];0.84[MKK][hapmap];0.81[AFR][1000 genomes]
rs8024139	0.81[AFR][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	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv903983	chr15:33388030-33550256	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2444961	GABRG3	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33419200-33427600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:33419200-33427600	Weak transcription	Lung	lung
3	chr15:33419200-33428600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:33419200-33430000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:33419200-33430400	Weak transcription	Psoas Muscle	Psoas
6	chr15:33420000-33427200	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:33420400-33426200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:33420600-33434800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:33423200-33425400	Enhancers	Fetal Thymus	thymus
10	chr15:33423600-33425400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr15:33423600-33425400	Enhancers	Hela-S3	cervix
12	chr15:33423600-33425400	Enhancers	NHEK	skin
13	chr15:33423600-33425600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:33423600-33425600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:33423600-33425600	Enhancers	HSMM	muscle
16	chr15:33423600-33425600	Enhancers	NHLF	lung
17	chr15:33423600-33428400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr15:33423600-33428800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:33423800-33425400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:33423800-33425400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:33423800-33425400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:33423800-33425400	Enhancers	Fetal Kidney	kidney
23	chr15:33423800-33425400	Enhancers	NHDF-Ad	bronchial
24	chr15:33423800-33425600	Enhancers	Fetal Muscle Leg	muscle
25	chr15:33423800-33425600	Enhancers	HSMMtube	muscle
26	chr15:33423800-33425600	Enhancers	Osteobl	bone
27	chr15:33424000-33425400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:33424400-33430000	Weak transcription	Fetal Lung	lung
29	chr15:33424400-33440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:33424600-33425400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:33424600-33429800	Weak transcription	Brain Angular Gyrus	brain
32	chr15:33424800-33425600	Enhancers	HMEC	breast
33	chr15:33424800-33427200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:33425000-33425400	Enhancers	Duodenum Mucosa	Duodenum
35	chr15:33425000-33425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:33425000-33425600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr15:33425000-33425600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:33425000-33430000	Weak transcription	Fetal Stomach	stomach
39	chr15:33425200-33425400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr15:33425200-33425400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:33425200-33425400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr15:33425200-33425600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr15:33425200-33425600	Enhancers	Adipose Nuclei	Adipose
44	chr15:33425200-33425800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:33425200-33425800	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links