Variant report

Variant	rs2289191
Chromosome Location	chr1:220300035-220300036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220292837..220298282-chr1:220298660..220304315,8	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1059140	0.92[AMR][1000 genomes]
rs11547779	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[AMR][1000 genomes]
rs12032345	0.92[AMR][1000 genomes]
rs2289189	0.83[AMR][1000 genomes]
rs2292418	0.91[AMR][1000 genomes]
rs3767655	0.83[AMR][1000 genomes]
rs41274790	0.80[AMR][1000 genomes]
rs41274794	0.84[AMR][1000 genomes]
rs41303055	0.83[AMR][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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2289191	RAB3GAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220268400-220330200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:220269400-220330000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:220278600-220316200	Weak transcription	Pancreas	Pancrea
4	chr1:220281400-220300600	Weak transcription	NHLF	lung
5	chr1:220281400-220307200	Weak transcription	Brain Angular Gyrus	brain
6	chr1:220281400-220307800	Weak transcription	Psoas Muscle	Psoas
7	chr1:220281400-220314400	Weak transcription	Fetal Brain Male	brain
8	chr1:220284600-220301400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:220284600-220305600	Weak transcription	Small Intestine	intestine
10	chr1:220284600-220307400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:220284600-220307800	Weak transcription	Spleen	Spleen
12	chr1:220284600-220313000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:220284600-220313600	Weak transcription	Gastric	stomach
14	chr1:220284600-220324600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:220284800-220301600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:220288200-220324600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:220288400-220310200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:220289400-220301600	Weak transcription	Esophagus	oesophagus
19	chr1:220289600-220301400	Weak transcription	Fetal Kidney	kidney
20	chr1:220289600-220301600	Weak transcription	Brain Substantia Nigra	brain
21	chr1:220289600-220307800	Weak transcription	Thymus	Thymus
22	chr1:220289800-220300400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:220289800-220300800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:220289800-220301800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:220289800-220306400	Weak transcription	NHEK	skin
26	chr1:220289800-220307400	Weak transcription	HSMMtube	muscle
27	chr1:220289800-220307800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:220290200-220300600	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:220290400-220300600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:220290400-220304600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:220290400-220307800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:220290800-220307800	Weak transcription	Lung	lung
33	chr1:220291000-220301400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:220291200-220314400	Weak transcription	NH-A	brain
35	chr1:220291400-220300600	Weak transcription	Fetal Brain Female	brain
36	chr1:220291400-220300800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:220291600-220300400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:220291600-220300400	Weak transcription	Brain Germinal Matrix	brain
39	chr1:220291600-220306200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:220291800-220300400	Weak transcription	HMEC	breast
41	chr1:220292000-220300600	Weak transcription	HSMM	muscle
42	chr1:220293200-220300400	Weak transcription	Hela-S3	cervix
43	chr1:220295200-220309000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:220295400-220300600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:220295400-220310600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:220295800-220306000	Weak transcription	Aorta	Aorta
47	chr1:220296000-220300800	Weak transcription	Brain Anterior Caudate	brain
48	chr1:220296000-220327600	Weak transcription	Colonic Mucosa	Colon
49	chr1:220296600-220323200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:220297200-220304400	Strong transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links