Variant report

Variant	rs2902811
Chromosome Location	chr1:151010521-151010522
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151008538..151012828-chr1:151019200..151022428,4	K562	blood:
2	chr1:151005028..151012583-chr1:151026392..151034442,13	K562	blood:
3	chr1:151008451..151011049-chr1:151011107..151015383,5	K562	blood:
4	chr1:150979416..150982558-chr1:151006468..151010604,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143409	Chromatin interaction
ENSG00000143443	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000213190	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10788797	0.91[ASN][1000 genomes]
rs15740	0.83[AMR][1000 genomes]
rs2091219	0.92[ASN][1000 genomes]
rs3738476	0.91[ASN][1000 genomes]
rs4589116	0.91[ASN][1000 genomes]
rs4970936	0.83[AMR][1000 genomes]
rs4970989	0.91[ASN][1000 genomes]
rs4970991	0.91[ASN][1000 genomes]
rs6587552	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6587553	0.81[AMR][1000 genomes]
rs6691701	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2902811	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL
rs2902811	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150997600-151015400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:150997600-151019800	Weak transcription	HUVEC	blood vessel
3	chr1:150997800-151019800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:151000000-151019800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:151000000-151019800	Weak transcription	NHLF	lung
6	chr1:151000200-151019800	Weak transcription	Small Intestine	intestine
7	chr1:151003000-151011400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:151003800-151019800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:151004400-151011400	Weak transcription	NHDF-Ad	bronchial
10	chr1:151004400-151015400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:151004400-151019800	Weak transcription	Fetal Kidney	kidney
12	chr1:151006800-151015400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:151006800-151019800	Weak transcription	Gastric	stomach
14	chr1:151006800-151019800	Weak transcription	HepG2	liver
15	chr1:151007000-151019000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:151007000-151019600	Weak transcription	Colonic Mucosa	Colon
17	chr1:151007200-151010600	Weak transcription	GM12878-XiMat	blood
18	chr1:151007200-151019800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:151007200-151019800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:151007400-151010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:151007400-151015400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:151007400-151019600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:151007400-151019800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:151007400-151019800	Weak transcription	Brain Angular Gyrus	brain
25	chr1:151007400-151019800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:151007600-151015400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:151007600-151019600	Weak transcription	Fetal Brain Male	brain
28	chr1:151007800-151015400	Weak transcription	Spleen	Spleen
29	chr1:151007800-151015600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:151007800-151019000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:151007800-151019000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:151007800-151019200	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:151008000-151015400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:151008000-151015400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:151008000-151015400	Weak transcription	HSMMtube	muscle
36	chr1:151008000-151015600	Weak transcription	Brain Substantia Nigra	brain
37	chr1:151008000-151018000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr1:151008000-151018000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr1:151008000-151019000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:151008000-151019200	Weak transcription	Primary B cells from cord blood	blood
41	chr1:151008000-151019200	Weak transcription	Dnd41	blood
42	chr1:151008000-151019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:151008000-151019600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:151008000-151019600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:151008000-151019600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:151008000-151019600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:151008000-151019600	Weak transcription	A549	lung
48	chr1:151008000-151019600	Weak transcription	Osteobl	bone
49	chr1:151008000-151019800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:151008000-151019800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links