Variant report

Variant	rs3780577
Chromosome Location	chr9:13211404-13211405
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:13171132..13173379-chr9:13209531..13212132,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10125695	0.89[ASN][1000 genomes]
rs10756460	0.90[EUR][1000 genomes]
rs10756461	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs10960970	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1331675	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1556421	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1999395	1.00[CEU][hapmap];0.84[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2225483	0.83[CEU][hapmap]
rs3780576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3780578	0.92[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs4741291	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs7040347	0.84[CEU][hapmap]
rs72706366	0.88[EUR][1000 genomes]
rs7863888	1.00[CEU][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv892583	chr9:13166139-13350478	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13121600-13225200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:13135400-13223600	Weak transcription	Lung	lung
3	chr9:13145400-13228600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:13164200-13248600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:13164200-13258800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:13182200-13226800	Weak transcription	Fetal Brain Male	brain
7	chr9:13186400-13212000	Weak transcription	Gastric	stomach
8	chr9:13188000-13220800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:13189000-13221000	Weak transcription	NHLF	lung
10	chr9:13189000-13268600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:13190400-13237800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:13195400-13223400	Weak transcription	Fetal Stomach	stomach
13	chr9:13202800-13215600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:13202800-13220800	Weak transcription	Placenta	Placenta
15	chr9:13202800-13226400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr9:13202800-13250600	Weak transcription	Pancreas	Pancrea
17	chr9:13202800-13250800	Weak transcription	Psoas Muscle	Psoas
18	chr9:13203000-13223600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr9:13203000-13224800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:13203000-13225400	Weak transcription	Brain Anterior Caudate	brain
21	chr9:13203000-13261000	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:13203200-13214400	Weak transcription	Fetal Brain Female	brain
23	chr9:13203400-13214000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:13203400-13223600	Weak transcription	Ovary	ovary
25	chr9:13203400-13224800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:13203400-13226400	Weak transcription	Right Ventricle	heart
27	chr9:13203400-13247000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr9:13203600-13216200	Weak transcription	Brain Substantia Nigra	brain
29	chr9:13203600-13219600	Weak transcription	HSMMtube	muscle
30	chr9:13203600-13245600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:13203800-13220800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:13204000-13215000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:13204000-13241800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:13204000-13249200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:13204200-13244600	Weak transcription	HepG2	liver
36	chr9:13204400-13212400	Weak transcription	Fetal Muscle Leg	muscle
37	chr9:13204400-13214400	Weak transcription	Brain Germinal Matrix	brain
38	chr9:13204400-13221800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:13204600-13214000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:13204800-13213600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:13206000-13212200	Weak transcription	HSMM	muscle
42	chr9:13206000-13212200	Weak transcription	NH-A	brain
43	chr9:13206000-13214000	Weak transcription	Fetal Kidney	kidney
44	chr9:13206000-13214800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:13206000-13218800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:13206000-13219400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr9:13206000-13223000	Weak transcription	Brain Hippocampus Middle	brain
48	chr9:13206000-13229200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr9:13206000-13247000	Weak transcription	Brain Angular Gyrus	brain
50	chr9:13206200-13212200	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links