Variant report

Variant	rs10878391
Chromosome Location	chr12:66561788-66561789
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66561525..66563608-chr12:66580703..66583177,2	K562	blood:
2	chr12:66523792..66527078-chr12:66561013..66565049,6	MCF-7	breast:
3	chr12:66523081..66526604-chr12:66560988..66564576,8	MCF-7	breast:
4	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:
5	chr12:66561184..66563224-chr12:66629023..66631827,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090376	Chromatin interaction
ENSG00000266539	Chromatin interaction
ENSG00000139233	Chromatin interaction
ENSG00000239335	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10400539	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10506478	0.85[EUR][1000 genomes]
rs10878381	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878382	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10878383	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10878389	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176043	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11176054	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176056	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176063	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176065	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176067	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176068	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176080	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176082	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12227630	0.82[EUR][1000 genomes]
rs12832926	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17767200	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1882201	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1898304	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1921083	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2141709	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2178486	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2870781	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34645929	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34755483	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4474482	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4575321	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56271210	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61927092	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7295147	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7302893	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7305938	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7966453	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7966561	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7979029	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7979775	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv541516	chr12:66547969-66596036	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv899215	chr12:66556960-66594134	Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10878391	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs10878391	RP11-745O10.2	cis	Artery Tibial	GTEx
rs10878391	RP11-745O10.2	cis	Thyroid	GTEx
rs10878391	RP11-745O10.2	cis	Whole Blood	GTEx
rs10878391	RP11-745O10.2	cis	lung	GTEx
rs10878391	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66525400-66562400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:66536400-66562400	Weak transcription	HMEC	breast
4	chr12:66539400-66562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:66542800-66563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:66547400-66562000	Weak transcription	HUVEC	blood vessel
7	chr12:66548400-66562200	Weak transcription	Brain Anterior Caudate	brain
8	chr12:66548600-66562000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:66549200-66561800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:66549200-66561800	Weak transcription	Right Atrium	heart
11	chr12:66553000-66562200	Weak transcription	Brain Angular Gyrus	brain
12	chr12:66553200-66562400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:66553800-66561800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:66554000-66561800	Weak transcription	HSMMtube	muscle
15	chr12:66554000-66562000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:66554000-66562000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:66554000-66562000	Weak transcription	NHEK	skin
18	chr12:66554000-66562000	Weak transcription	Osteobl	bone
19	chr12:66554000-66562200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:66554000-66562200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:66554000-66562200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:66554000-66562200	Weak transcription	NHLF	lung
23	chr12:66554000-66562400	Weak transcription	Brain Germinal Matrix	brain
24	chr12:66554000-66563000	Weak transcription	Gastric	stomach
25	chr12:66554200-66562200	Weak transcription	NH-A	brain
26	chr12:66554400-66562000	Weak transcription	Fetal Kidney	kidney
27	chr12:66554600-66562000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:66554800-66561800	Weak transcription	Pancreas	Pancrea
29	chr12:66554800-66562200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:66555000-66561800	Weak transcription	Fetal Thymus	thymus
31	chr12:66555000-66562200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:66555000-66562600	Weak transcription	Aorta	Aorta
33	chr12:66555000-66562800	Weak transcription	Esophagus	oesophagus
34	chr12:66555200-66562200	Weak transcription	Fetal Stomach	stomach
35	chr12:66556400-66562400	Weak transcription	Spleen	Spleen
36	chr12:66556600-66562200	Weak transcription	Brain Substantia Nigra	brain
37	chr12:66557000-66562800	Weak transcription	Ovary	ovary
38	chr12:66557400-66561800	Weak transcription	Right Ventricle	heart
39	chr12:66558200-66561800	Weak transcription	Psoas Muscle	Psoas
40	chr12:66558200-66562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:66558400-66562400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:66558600-66561800	Weak transcription	K562	blood
43	chr12:66559400-66561800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:66559400-66562400	Weak transcription	Colonic Mucosa	Colon
45	chr12:66559400-66563000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:66559600-66562000	Weak transcription	Fetal Intestine Large	intestine
47	chr12:66559600-66562200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:66559800-66562000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:66560200-66561800	Weak transcription	Thymus	Thymus
50	chr12:66560200-66562200	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links