Variant report

Variant	rs11189206
Chromosome Location	chr10:99167802-99167803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99165782..99177128-chr10:99179856..99189832,30	MCF-7	breast:
2	chr10:99166608..99167808-chr10:99223063..99223942,3	K562	blood:
3	chr10:99165638..99168564-chr10:99206419..99208887,2	K562	blood:
4	chr10:99167329..99170303-chr10:99178953..99180930,2	K562	blood:
5	chr10:99159230..99162370-chr10:99166178..99169290,4	K562	blood:
6	chr10:99166902..99167876-chr10:99185470..99186302,2	MCF-7	breast:
7	chr10:99092178..99094562-chr10:99167092..99169004,2	MCF-7	breast:
8	chr10:99160158..99162662-chr10:99167761..99169476,2	K562	blood:
9	chr10:99167036..99170302-chr10:99173339..99176571,3	MCF-7	breast:
10	chr10:99166045..99168504-chr10:99170322..99173005,2	K562	blood:
11	chr10:99166916..99167827-chr10:99185028..99186031,4	K562	blood:
12	chr10:99166882..99167838-chr10:99223370..99224268,2	MCF-7	breast:
13	chr10:99167024..99167842-chr10:99193469..99194416,4	MCF-7	breast:
14	chr10:99167020..99167837-chr10:99221428..99222089,2	K562	blood:
15	chr10:99164883..99168740-chr10:99185841..99188732,4	K562	blood:
16	chr10:99167747..99170750-chr10:99204032..99206080,4	MCF-7	breast:
17	chr10:99166892..99169975-chr10:99170359..99172836,3	MCF-7	breast:
18	chr10:99167117..99169184-chr10:99173224..99175033,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000155229	Chromatin interaction
ENSG00000225850	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000231970	Chromatin interaction
ENSG00000052749	Chromatin interaction
ENSG00000224474	Chromatin interaction
ENSG00000181274	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000200737	Chromatin interaction
ENSG00000171314	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10444013	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10444014	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444016	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048442	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10786336	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10786337	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10786338	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10786339	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10786340	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10786341	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10786342	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10786343	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10786344	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786345	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786347	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10882903	0.84[CEU][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882904	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs10882907	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs10882908	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10882909	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882910	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882911	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882912	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882913	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882914	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882915	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882916	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882917	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10882922	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10882924	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882926	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10882929	0.84[AMR][1000 genomes]
rs10882930	0.84[AMR][1000 genomes]
rs10882931	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882934	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189144	0.81[EUR][1000 genomes]
rs11189165	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs11189168	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs11189172	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs11189173	0.83[CEU][hapmap]
rs11189174	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189175	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189177	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189178	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189179	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189180	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189181	0.85[EUR][1000 genomes]
rs11189182	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11189183	0.87[EUR][1000 genomes]
rs11189191	0.91[EUR][1000 genomes]
rs11189192	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11189195	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11189196	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11189197	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11189200	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11189204	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189208	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11812223	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11814021	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11817852	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11817875	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12258560	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12266723	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12359257	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1537645	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1537646	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17112674	0.87[CEU][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17112676	0.85[EUR][1000 genomes]
rs1810983	0.84[EUR][1000 genomes]
rs1932001	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs2275089	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2275090	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2297667	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297668	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2297988	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs3737194	0.86[CEU][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3814553	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818787	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3818908	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4635018	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60237341	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61861912	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61863813	0.81[EUR][1000 genomes]
rs61863815	0.85[EUR][1000 genomes]
rs61863819	0.89[EUR][1000 genomes]
rs6584126	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6584127	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6584128	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7074511	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7078004	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7078782	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084654	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7088410	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7092350	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7092499	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7096801	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7895695	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7896100	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7903562	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7909345	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7916665	0.80[AMR][1000 genomes]
rs7918742	0.83[EUR][1000 genomes]
rs7921585	0.83[EUR][1000 genomes]
rs7922512	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7923385	0.84[CEU][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs869967	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs954149	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs9787426	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9787454	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9887991	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9887994	0.80[AMR][1000 genomes]
rs9888026	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9888116	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9888117	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][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	nsv467438	chr10:99126249-99173870	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv552024	chr10:99126249-99173870	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv467440	chr10:99134784-99204791	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv552025	chr10:99134784-99204791	Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11189206	RRP12	cis	Heart Left Ventricle	GTEx
rs11189206	RRP12	cis	Muscle Skeletal	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99161600-99178800	Weak transcription	Fetal Stomach	stomach
2	chr10:99161600-99185200	Weak transcription	Pancreas	Pancrea
3	chr10:99164200-99170200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr10:99165000-99169400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr10:99165400-99168000	Enhancers	Primary hematopoietic stem cells	blood
6	chr10:99165400-99168800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr10:99165800-99169000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:99166000-99168600	Enhancers	NHEK	skin
9	chr10:99166000-99168800	Enhancers	HMEC	breast
10	chr10:99166400-99169000	Enhancers	Placenta	Placenta
11	chr10:99166600-99169000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:99166800-99168800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr10:99167000-99168000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr10:99167000-99168800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:99167000-99169000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr10:99167200-99168000	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr10:99167200-99168600	Enhancers	Stomach Mucosa	stomach
18	chr10:99167200-99169800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr10:99167400-99168000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:99167400-99168000	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr10:99167400-99168600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr10:99167400-99168600	Flanking Active TSS	HepG2	liver
23	chr10:99167400-99168800	Enhancers	Duodenum Mucosa	Duodenum
24	chr10:99167400-99169600	Enhancers	Primary B cells from cord blood	blood
25	chr10:99167400-99171200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:99167400-99171200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:99167400-99171200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr10:99167400-99172400	Weak transcription	Primary T cells from cord blood	blood
29	chr10:99167400-99174000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:99167400-99174800	Weak transcription	NHDF-Ad	bronchial
31	chr10:99167400-99176200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr10:99167400-99178000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr10:99167400-99179000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr10:99167400-99185200	Weak transcription	Fetal Lung	lung
35	chr10:99167400-99185400	Weak transcription	Gastric	stomach
36	chr10:99167600-99168600	Weak transcription	Spleen	Spleen
37	chr10:99167600-99168600	Enhancers	K562	blood
38	chr10:99167600-99168800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:99167600-99170800	Weak transcription	Fetal Heart	heart
40	chr10:99167600-99171000	Weak transcription	NH-A	brain
41	chr10:99167600-99171000	Weak transcription	Osteobl	bone
42	chr10:99167600-99171200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr10:99167600-99171200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr10:99167600-99171200	Weak transcription	Fetal Kidney	kidney
45	chr10:99167600-99172400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr10:99167600-99172400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr10:99167600-99172400	Weak transcription	GM12878-XiMat	blood
48	chr10:99167600-99172600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr10:99167600-99172600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr10:99167600-99172600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links