Variant report

Variant	rs1821777
Chromosome Location	chr12:66606228-66606229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10506480	0.81[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs11465955	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11465970	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179917	0.80[EUR][1000 genomes]
rs17767286	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17767298	0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1882200	0.91[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293657	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782347	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4762087	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4762088	0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55715236	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55913894	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56156535	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56365678	0.81[EUR][1000 genomes]
rs61927088	0.89[EUR][1000 genomes]
rs61927090	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7302556	0.80[CEU][hapmap];0.88[TSI][hapmap];0.82[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	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv541517	chr12:66576953-66639823	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1821777	TMBIM4	cis	cerebellum	SCAN
rs1821777	TMBIM4	cis	parietal	SCAN
rs1821777	MDM1	cis	parietal	SCAN
rs1821777	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66583800-66623400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:66589600-66623400	Weak transcription	Spleen	Spleen
3	chr12:66592400-66628400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:66593400-66613400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:66597600-66623400	Weak transcription	Aorta	Aorta
6	chr12:66597800-66609000	Weak transcription	Stomach Mucosa	stomach
7	chr12:66599000-66608800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:66604000-66620200	Weak transcription	Lung	lung
9	chr12:66604400-66628800	Weak transcription	Right Ventricle	heart
10	chr12:66604800-66609000	Strong transcription	Left Ventricle	heart
11	chr12:66604800-66610600	Strong transcription	Fetal Lung	lung
12	chr12:66605200-66628800	Weak transcription	Psoas Muscle	Psoas
13	chr12:66605400-66606800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:66605400-66609000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:66605400-66628200	Weak transcription	NHDF-Ad	bronchial
16	chr12:66605600-66606800	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:66605600-66607000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:66605600-66607200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:66605600-66611400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:66605800-66608000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:66606000-66606800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:66606000-66606800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:66606000-66606800	Strong transcription	Adipose Nuclei	Adipose
24	chr12:66606000-66609200	Strong transcription	Primary hematopoietic stem cells	blood
25	chr12:66606000-66610400	Weak transcription	Primary B cells from cord blood	blood
26	chr12:66606200-66606400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:66606200-66606600	Enhancers	NHEK	skin
28	chr12:66606200-66607600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:66606200-66608800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr12:66606200-66609400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr12:66606200-66609800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:66606200-66610600	Weak transcription	Primary B cells from peripheral blood	blood

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