Variant report

Variant	rs11169710
Chromosome Location	chr12:51503442-51503443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10275	0.83[EUR][1000 genomes]
rs10783409	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10783413	0.89[ASN][1000 genomes]
rs10876127	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876128	0.83[EUR][1000 genomes]
rs10876129	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876130	0.85[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10876131	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs10876132	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10876136	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876138	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs10876139	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169695	0.84[EUR][1000 genomes]
rs11169707	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610644	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12370120	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12379	1.00[CHB][hapmap]
rs12424509	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12427345	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1466579	0.87[ASN][1000 genomes]
rs1486014	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs15756	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1632791	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs17125111	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs17125340	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2029145	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2029146	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs224572	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2730655	0.96[ASN][1000 genomes]
rs370462	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs3759405	1.00[CHB][hapmap]
rs427020	1.00[CHB][hapmap]
rs4438107	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55874804	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61934800	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580782	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580785	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580788	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6580791	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs7135399	0.82[ASN][1000 genomes]
rs7136960	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7953867	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs7958068	0.88[EUR][1000 genomes]
rs7969803	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971308	1.00[CHB][hapmap]
rs7976431	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs901313	0.87[ASN][1000 genomes]
rs9739342	0.84[EUR][1000 genomes];0.82[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11169710	LETMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477400-51518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51477800-51518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:51477800-51518400	Weak transcription	Pancreas	Pancrea
4	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:51483800-51513400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:51484400-51506000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:51484800-51507000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:51485000-51507600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr12:51485000-51513200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:51485800-51513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:51486000-51511400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:51486400-51510800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:51486600-51508000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:51486800-51504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:51486800-51508000	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr12:51487000-51505000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:51487000-51506600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:51487000-51511400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:51487200-51505000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:51487200-51508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr12:51487200-51513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:51487200-51513200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:51487400-51511000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:51487600-51504800	Strong transcription	Adipose Nuclei	Adipose
26	chr12:51487600-51508200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:51487600-51512000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr12:51487800-51505000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:51487800-51505600	Strong transcription	Liver	Liver
30	chr12:51488000-51507600	Strong transcription	Fetal Intestine Large	intestine
31	chr12:51488400-51526600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:51489200-51509400	Weak transcription	Fetal Heart	heart
33	chr12:51493600-51512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:51494400-51515600	Weak transcription	Stomach Mucosa	stomach
35	chr12:51494600-51518200	Weak transcription	Esophagus	oesophagus
36	chr12:51494800-51518400	Weak transcription	Aorta	Aorta
37	chr12:51495000-51504000	Weak transcription	Gastric	stomach
38	chr12:51496400-51523400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:51497000-51504600	Strong transcription	Hela-S3	cervix
40	chr12:51498000-51504000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:51498800-51505000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:51499000-51503600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:51499000-51503600	Strong transcription	HSMM	muscle
44	chr12:51499000-51504800	Strong transcription	Dnd41	blood
45	chr12:51499000-51507600	Strong transcription	Fetal Lung	lung
46	chr12:51499000-51510200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:51499200-51504800	Strong transcription	Osteobl	bone
48	chr12:51499200-51505200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:51499200-51508000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:51499200-51508200	Strong transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links