Variant report

Variant	rs6580788
Chromosome Location	chr12:51495292-51495293
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10275	0.92[EUR][1000 genomes]
rs10783409	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10783413	0.89[ASN][1000 genomes]
rs10876127	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876128	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs10876129	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876130	0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10876131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10876132	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10876136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876138	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs10876139	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169657	0.81[EUR][1000 genomes]
rs11169695	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11169707	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169710	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];1.00[ASN][1000 genomes]
rs11610644	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12370120	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12379	1.00[CHB][hapmap]
rs12424509	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs12427345	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1466579	0.87[ASN][1000 genomes]
rs1486014	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs15756	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1632791	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs17125111	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs17125340	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2029145	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2029146	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs224448	0.81[EUR][1000 genomes]
rs224572	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs224575	0.81[CEU][hapmap]
rs2730655	0.96[ASN][1000 genomes]
rs319936	0.81[CEU][hapmap]
rs319939	0.81[CEU][hapmap]
rs370462	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs3759405	1.00[CHB][hapmap]
rs427020	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4438107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55874804	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61934800	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580782	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580791	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs706805	0.80[EUR][1000 genomes]
rs7135399	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7136960	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7953867	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs7958068	0.98[EUR][1000 genomes]
rs7969803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971308	1.00[CHB][hapmap]
rs7976431	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs901313	0.87[ASN][1000 genomes]
rs9739342	0.83[AMR][1000 genomes];0.93[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
rs6580788	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	chr12:51477800-51499600	Weak transcription	NHLF	lung
3	chr12:51477800-51518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:51477800-51518400	Weak transcription	Pancreas	Pancrea
5	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:51478000-51496000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:51482800-51498000	Strong transcription	Fetal Muscle Leg	muscle
8	chr12:51482800-51499400	Strong transcription	Fetal Stomach	stomach
9	chr12:51483800-51513400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:51484000-51502000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:51484400-51506000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:51484800-51507000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:51485000-51498400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:51485000-51507600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:51485000-51513200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:51485600-51498200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr12:51485600-51498200	Strong transcription	Fetal Thymus	thymus
19	chr12:51485800-51497400	Strong transcription	Fetal Intestine Small	intestine
20	chr12:51485800-51513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:51486000-51511400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:51486400-51510800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:51486600-51508000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:51486800-51497800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:51486800-51504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:51486800-51508000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:51487000-51498200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:51487000-51505000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:51487000-51506600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:51487000-51511400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:51487200-51498000	Strong transcription	Osteobl	bone
32	chr12:51487200-51498200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:51487200-51498400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:51487200-51502000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr12:51487200-51505000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:51487200-51508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:51487200-51513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:51487200-51513200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:51487400-51496400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr12:51487400-51498200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:51487400-51511000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:51487600-51498000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:51487600-51498000	Strong transcription	Primary T cells from cord blood	blood
44	chr12:51487600-51498000	Strong transcription	Brain Anterior Caudate	brain
45	chr12:51487600-51498200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:51487600-51498400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr12:51487600-51498400	Strong transcription	Placenta	Placenta
48	chr12:51487600-51504800	Strong transcription	Adipose Nuclei	Adipose
49	chr12:51487600-51508200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:51487600-51512000	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links