Variant report

Variant	rs10876132
Chromosome Location	chr12:51468646-51468647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51459276..51461108-chr12:51467854..51469536,2	MCF-7	breast:
2	chr12:51441202..51443113-chr12:51468336..51471322,2	K562	blood:
3	chr12:51468579..51474515-chr12:51475298..51478642,16	K562	blood:
4	chr12:51466772..51468865-chr12:51469578..51471414,2	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000050426	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10275	0.97[EUR][1000 genomes]
rs10783409	0.81[ASN][1000 genomes]
rs10876127	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876128	0.98[EUR][1000 genomes]
rs10876129	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876130	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10876131	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876136	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10876139	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1095999	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169657	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169695	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169707	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11169710	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11610644	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12370120	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12379	0.84[ASN][1000 genomes]
rs12424509	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12427345	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1486014	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs15756	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1632791	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17125111	0.81[ASN][1000 genomes]
rs2010630	0.82[ASN][1000 genomes]
rs2029145	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2029146	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs224448	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs224572	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2554863	0.81[ASN][1000 genomes]
rs2630371	0.81[ASN][1000 genomes]
rs370462	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759405	0.84[ASN][1000 genomes]
rs427020	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4438107	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4768947	0.81[ASN][1000 genomes]
rs55874804	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61934800	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580782	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580785	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs706805	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7135399	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7136960	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7958068	0.92[EUR][1000 genomes]
rs7961626	0.83[EUR][1000 genomes]
rs7969803	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7971308	0.84[ASN][1000 genomes]
rs7976431	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7977740	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829025	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9739342	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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
rs10876132	LETMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51442800-51470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:51443400-51476000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:51444200-51470400	Strong transcription	Fetal Stomach	stomach
4	chr12:51445400-51469200	Strong transcription	Fetal Thymus	thymus
5	chr12:51445400-51470600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:51445600-51469200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:51445600-51469800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:51445600-51470400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:51445600-51470600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:51449800-51470000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:51453400-51470600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:51454000-51475400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:51454200-51470400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:51454200-51475600	Weak transcription	Stomach Mucosa	stomach
15	chr12:51455400-51470400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:51455400-51470800	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:51455600-51470400	Strong transcription	Brain Germinal Matrix	brain
18	chr12:51456400-51470400	Strong transcription	Fetal Intestine Small	intestine
19	chr12:51459000-51471400	Weak transcription	Fetal Heart	heart
20	chr12:51459000-51475600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:51459800-51469400	Weak transcription	Small Intestine	intestine
22	chr12:51459800-51475800	Weak transcription	GM12878-XiMat	blood
23	chr12:51461800-51475200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:51462000-51469800	Weak transcription	Psoas Muscle	Psoas
25	chr12:51462000-51475800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:51462000-51475800	Weak transcription	Pancreas	Pancrea
27	chr12:51462000-51476400	Weak transcription	Gastric	stomach
28	chr12:51462600-51474400	Weak transcription	Fetal Kidney	kidney
29	chr12:51463600-51468800	Strong transcription	Dnd41	blood
30	chr12:51463600-51470000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:51463800-51470200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:51463800-51470400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:51463800-51470600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:51464200-51470800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:51464400-51470000	Weak transcription	K562	blood
36	chr12:51464400-51475800	Weak transcription	HMEC	breast
37	chr12:51464600-51470000	Strong transcription	Lung	lung
38	chr12:51464800-51475800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:51465200-51469800	Strong transcription	Placenta	Placenta
40	chr12:51465600-51469200	Strong transcription	Fetal Muscle Leg	muscle
41	chr12:51465800-51469600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:51465800-51471400	Weak transcription	Fetal Brain Male	brain
43	chr12:51465800-51471800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr12:51466000-51468800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr12:51466000-51469000	Weak transcription	Brain Substantia Nigra	brain
46	chr12:51466000-51469400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:51466000-51470000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:51466000-51470600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:51466000-51471400	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:51466000-51471800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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