Variant report

Variant	rs10506478
Chromosome Location	chr12:66509607-66509608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66508864..66512065-chr12:66524248..66527368,3	K562	blood:

Variant related genes	Relation type
ENSG00000139233	Chromatin interaction
ENSG00000239335	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10400539	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10878381	0.92[CEU][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10878382	0.92[CEU][hapmap];0.91[CHD][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10878383	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10878389	0.91[CHD][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs10878391	0.85[EUR][1000 genomes]
rs11176043	0.92[CEU][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11176054	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11176056	0.92[CEU][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11176063	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11176065	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11176067	0.84[EUR][1000 genomes]
rs11176068	0.84[EUR][1000 genomes]
rs11176078	0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12227630	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12832926	0.92[CEU][hapmap];0.91[CHD][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17767200	0.92[CEU][hapmap];0.91[CHD][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1882201	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1898304	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1921083	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2141709	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2178486	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2870781	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34645929	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34755483	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4474482	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4575321	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56271210	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7295147	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7302893	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7305938	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7966453	0.82[EUR][1000 genomes]
rs7966561	0.82[EUR][1000 genomes]
rs7979029	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7979775	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10506478	RP11-745O10.2	cis	Thyroid	GTEx
rs10506478	TMBIM4	cis	parietal	SCAN
rs10506478	TMBIM4	cis	normal skin	skin_eQTL
rs10506478	TMBIM4	cis	uninvolved skin	skin_eQTL
rs10506478	TMBIM4	cis	cerebellum	SCAN
rs10506478	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10506478	RP11-745O10.2	cis	Whole Blood	GTEx
rs10506478	TMBIM4	cis	lymphoblastoid	seeQTL
rs10506478	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs10506478	TMBIM4	cis	lesional skin	skin_eQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66501200-66516000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:66501400-66514600	Weak transcription	A549	lung
3	chr12:66501400-66515400	Weak transcription	Liver	Liver
4	chr12:66501600-66512200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:66501600-66513000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:66501600-66513200	Weak transcription	Brain Anterior Caudate	brain
7	chr12:66501600-66513200	Weak transcription	HSMM	muscle
8	chr12:66501600-66513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:66501600-66513800	Weak transcription	Adipose Nuclei	Adipose
10	chr12:66501600-66514600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:66501600-66514600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:66501600-66514600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:66501600-66516000	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:66501600-66517600	Weak transcription	Right Ventricle	heart
15	chr12:66501800-66512400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:66501800-66516800	Weak transcription	NHEK	skin
17	chr12:66502000-66513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:66502000-66518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:66502400-66515800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:66502400-66516000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:66502400-66518400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:66502600-66516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:66502600-66516200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:66505400-66516000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:66505600-66512600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:66505800-66514600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:66505800-66515600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:66506400-66514000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:66506400-66516400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:66507800-66512400	Weak transcription	Primary T cells from cord blood	blood
31	chr12:66507800-66514600	Weak transcription	Thymus	Thymus
32	chr12:66508600-66515400	Weak transcription	Fetal Brain Female	brain
33	chr12:66509000-66514000	Weak transcription	Fetal Muscle Leg	muscle
34	chr12:66509000-66514400	Weak transcription	Left Ventricle	heart
35	chr12:66509000-66515200	Weak transcription	Lung	lung
36	chr12:66509000-66518200	Weak transcription	Esophagus	oesophagus
37	chr12:66509000-66519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:66509000-66523800	Weak transcription	Pancreas	Pancrea
39	chr12:66509200-66513800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:66509200-66515800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr12:66509200-66523600	Weak transcription	Gastric	stomach
42	chr12:66509400-66512400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:66509600-66513400	Weak transcription	Primary B cells from cord blood	blood
44	chr12:66509600-66518000	Weak transcription	Ovary	ovary

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