Variant report

Variant	rs10878389
Chromosome Location	chr12:66557817-66557818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66548703..66551216-chr12:66555058..66558052,2	MCF-7	breast:
2	chr12:66550852..66561080-chr12:66561565..66565303,15	MCF-7	breast:
3	chr12:66556389..66558004-chr12:66572118..66574414,2	MCF-7	breast:
4	chr12:66520160..66522337-chr12:66557451..66559274,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10400539	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10506478	0.91[CHD][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs10735933	0.81[CHB][hapmap]
rs10878381	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878382	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10878383	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10878391	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176043	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11176054	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176056	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176063	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176065	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176078	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs11176080	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176081	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs11176082	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12227630	0.81[EUR][1000 genomes]
rs12832926	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17767200	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1882201	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1898304	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1921083	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2141709	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2178486	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2870781	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34645929	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34755483	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4474482	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4575321	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56271210	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61927092	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7295147	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7302893	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7305938	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7966453	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7966561	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7979029	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7979775	0.96[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10878389	TMBIM4	cis	normal skin	skin_eQTL
rs10878389	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs10878389	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10878389	RP11-745O10.2	cis	lung	GTEx
rs10878389	RP11-745O10.2	cis	Artery Tibial	GTEx
rs10878389	TMBIM4	cis	lesional skin	skin_eQTL
rs10878389	RP11-745O10.2	cis	Thyroid	GTEx
rs10878389	TMBIM4	cis	cerebellum	SCAN
rs10878389	TMBIM4	cis	parietal	SCAN
rs10878389	FLJ23235	trans	multi-tissue	Pritchard
rs10878389	LLPH	cis	cerebellum	SCAN
rs10878389	TMBIM4	cis	uninvolved skin	skin_eQTL
rs10878389	RP11-745O10.2	cis	Whole Blood	GTEx
rs10878389	TMBIM4	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 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	chr12:66536200-66558000	Weak transcription	Fetal Brain Female	brain
4	chr12:66536400-66562400	Weak transcription	HMEC	breast
5	chr12:66538600-66560400	Weak transcription	Fetal Brain Male	brain
6	chr12:66539200-66558400	Weak transcription	A549	lung
7	chr12:66539400-66561400	Weak transcription	Fetal Heart	heart
8	chr12:66539400-66562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:66542800-66563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:66547400-66562000	Weak transcription	HUVEC	blood vessel
11	chr12:66548400-66562200	Weak transcription	Brain Anterior Caudate	brain
12	chr12:66548600-66562000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:66549200-66561800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:66549200-66561800	Weak transcription	Right Atrium	heart
15	chr12:66550400-66559200	Weak transcription	Colonic Mucosa	Colon
16	chr12:66551200-66560400	Weak transcription	HepG2	liver
17	chr12:66551400-66558000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr12:66553000-66562200	Weak transcription	Brain Angular Gyrus	brain
19	chr12:66553200-66561600	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:66553200-66562400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:66553400-66559000	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:66553800-66559200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:66553800-66561800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:66554000-66558600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:66554000-66558600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:66554000-66559200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:66554000-66560400	Weak transcription	HSMM	muscle
28	chr12:66554000-66560600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:66554000-66560800	Weak transcription	Liver	Liver
30	chr12:66554000-66561000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:66554000-66561200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:66554000-66561800	Weak transcription	HSMMtube	muscle
33	chr12:66554000-66562000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:66554000-66562000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:66554000-66562000	Weak transcription	NHEK	skin
36	chr12:66554000-66562000	Weak transcription	Osteobl	bone
37	chr12:66554000-66562200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:66554000-66562200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:66554000-66562200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:66554000-66562200	Weak transcription	NHLF	lung
41	chr12:66554000-66562400	Weak transcription	Brain Germinal Matrix	brain
42	chr12:66554000-66563000	Weak transcription	Gastric	stomach
43	chr12:66554200-66558000	Weak transcription	NHDF-Ad	bronchial
44	chr12:66554200-66561000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:66554200-66562200	Weak transcription	NH-A	brain
46	chr12:66554400-66561000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:66554400-66562000	Weak transcription	Fetal Kidney	kidney
48	chr12:66554600-66560400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr12:66554600-66562000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:66554800-66561800	Weak transcription	Pancreas	Pancrea

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