Variant report

Variant	rs1168762
Chromosome Location	chr12:66596709-66596710
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1152906	0.81[EUR][1000 genomes]
rs1152908	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1152909	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168641	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168642	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168643	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1168644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1168647	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1168648	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1168771	0.84[CEU][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1168774	0.83[TSI][hapmap]
rs1370127	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1370128	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1623665	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1624395	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1732877	0.94[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];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	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
5	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
rs1168762	MDM1	cis	parietal	SCAN
rs1168762	TMBIM4	cis	parietal	SCAN
rs1168762	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs1168762	TMBIM4	cis	cerebellum	SCAN

Chromatin state (count:19 , 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	chr12:66589400-66606000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:66589600-66623400	Weak transcription	Spleen	Spleen
4	chr12:66591400-66597000	Weak transcription	Stomach Mucosa	stomach
5	chr12:66592200-66598000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:66592200-66604400	Weak transcription	NHDF-Ad	bronchial
7	chr12:66592200-66606000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:66592400-66603400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:66592400-66628400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:66593400-66606000	Weak transcription	Adipose Nuclei	Adipose
11	chr12:66593400-66613400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:66593800-66598400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:66594200-66597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:66594400-66598200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:66594400-66598800	Weak transcription	Fetal Lung	lung
16	chr12:66594600-66597400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:66594600-66603800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:66595400-66597200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:66595600-66597600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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