Variant report

Variant	rs1921080
Chromosome Location	chr12:66522913-66522914
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:145096186..145098889-chr12:66522673..66525529,2	MCF-7	breast:
2	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction
ENSG00000223380	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10459263	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10506475	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10506479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878379	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878380	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878384	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];0.99[ASN][1000 genomes]
rs10878387	0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176040	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176041	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176042	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176044	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176046	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176047	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];0.99[ASN][1000 genomes]
rs11176048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176059	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168744	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]
rs1168757	0.93[GIH][hapmap]
rs1168758	0.80[CEU][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1168771	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1168772	0.80[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1179914	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs12230221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12306484	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs12423372	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12426813	0.90[EUR][1000 genomes]
rs12578364	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12578752	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs12578754	0.90[EUR][1000 genomes]
rs12578801	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs12578994	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs12581033	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];0.99[ASN][1000 genomes]
rs12581836	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582384	1.00[CEU][hapmap];0.95[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];0.99[ASN][1000 genomes]
rs12814331	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12814606	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12821415	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12822410	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823414	0.85[EUR][1000 genomes]
rs12823732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12825992	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1625441	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs17245364	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1732893	0.89[CEU][hapmap];0.96[GIH][hapmap]
rs17825931	0.85[CHB][hapmap]
rs17825943	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1921082	0.89[CEU][hapmap];0.96[GIH][hapmap]
rs2701653	0.93[GIH][hapmap]
rs2870786	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];1.00[ASN][1000 genomes]
rs2904498	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34406211	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34552143	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35085853	0.84[EUR][1000 genomes]
rs35131575	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35187440	0.93[EUR][1000 genomes]
rs35447479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35971570	0.93[EUR][1000 genomes]
rs36073795	0.93[EUR][1000 genomes]
rs4281516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57825508	0.88[ASN][1000 genomes]
rs59112451	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60102429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66767092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71450848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73315943	0.90[EUR][1000 genomes]
rs737614	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv899214	chr12:66516692-66556960	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1921080	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66509000-66523800	Weak transcription	Pancreas	Pancrea
2	chr12:66509200-66523600	Weak transcription	Gastric	stomach
3	chr12:66513600-66523400	Weak transcription	Small Intestine	intestine
4	chr12:66513600-66523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:66514200-66523200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:66514400-66523800	Weak transcription	Spleen	Spleen
7	chr12:66515600-66523000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:66515600-66523600	Weak transcription	Lung	lung
9	chr12:66516000-66524000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:66516600-66523800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:66516800-66523600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:66516800-66523600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:66517200-66523400	Weak transcription	Stomach Mucosa	stomach
14	chr12:66518400-66523600	Weak transcription	Right Atrium	heart
15	chr12:66518600-66523400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:66518800-66523600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:66518800-66523600	Weak transcription	Psoas Muscle	Psoas
18	chr12:66518800-66523600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:66519000-66523400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:66519000-66523600	Weak transcription	Fetal Kidney	kidney
21	chr12:66519000-66523600	Weak transcription	Right Ventricle	heart
22	chr12:66519000-66523800	Weak transcription	Aorta	Aorta
23	chr12:66519400-66523400	Weak transcription	HSMMtube	muscle
24	chr12:66519600-66523400	Weak transcription	Brain Substantia Nigra	brain
25	chr12:66520000-66523600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:66520800-66523400	Weak transcription	Fetal Intestine Small	intestine
27	chr12:66521000-66523400	Enhancers	Fetal Heart	heart
28	chr12:66521200-66523000	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:66521400-66523000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:66521400-66523400	Weak transcription	Colonic Mucosa	Colon
31	chr12:66521400-66523800	Weak transcription	Esophagus	oesophagus
32	chr12:66521800-66523000	Weak transcription	NHEK	skin
33	chr12:66521800-66523400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:66521800-66523600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:66522000-66523200	Weak transcription	Brain Anterior Caudate	brain
36	chr12:66522000-66523200	Weak transcription	Fetal Stomach	stomach
37	chr12:66522000-66523200	Weak transcription	HUVEC	blood vessel
38	chr12:66522000-66523400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:66522000-66523400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:66522000-66523600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:66522200-66523400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:66522200-66523400	Weak transcription	Brain Angular Gyrus	brain
43	chr12:66522200-66523400	Enhancers	HepG2	liver
44	chr12:66522400-66523000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:66522400-66523000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr12:66522400-66523000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:66522400-66523000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:66522400-66523000	Weak transcription	Hela-S3	cervix
49	chr12:66522400-66523000	Weak transcription	HMEC	breast
50	chr12:66522400-66523000	Weak transcription	K562	blood

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