Variant report

Variant	rs1623665
Chromosome Location	chr12:66618182-66618183
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1152906	0.82[EUR][1000 genomes]
rs1152908	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1152909	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168641	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1168642	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1168647	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168648	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168762	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]
rs1168771	0.84[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1168774	0.83[TSI][hapmap]
rs1370127	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370128	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];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1624395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732877	1.00[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][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
rs1623665	MDM1	cis	parietal	SCAN
rs1623665	TMBIM4	cis	parietal	SCAN
rs1623665	TMBIM4	cis	cerebellum	SCAN
rs1623665	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 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	chr12:66597600-66623400	Weak transcription	Aorta	Aorta
5	chr12:66604000-66620200	Weak transcription	Lung	lung
6	chr12:66604400-66628800	Weak transcription	Right Ventricle	heart
7	chr12:66605200-66628800	Weak transcription	Psoas Muscle	Psoas
8	chr12:66605400-66628200	Weak transcription	NHDF-Ad	bronchial
9	chr12:66606400-66620000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:66606800-66623000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:66606800-66625800	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:66608800-66628800	Weak transcription	Gastric	stomach
13	chr12:66609000-66628800	Weak transcription	Left Ventricle	heart
14	chr12:66609200-66628800	Weak transcription	Colonic Mucosa	Colon
15	chr12:66609200-66629000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:66609400-66626200	Weak transcription	Small Intestine	intestine
17	chr12:66610000-66628800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:66611600-66627600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:66612000-66626600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:66612200-66628000	Weak transcription	Placenta	Placenta
21	chr12:66612400-66628200	Weak transcription	Primary B cells from cord blood	blood
22	chr12:66612600-66628000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:66613400-66628400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:66614000-66620000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:66614000-66620200	Weak transcription	Fetal Lung	lung
26	chr12:66614000-66621800	Weak transcription	Adipose Nuclei	Adipose
27	chr12:66614200-66627200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:66614200-66628000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:66614400-66622600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:66615600-66643400	Weak transcription	Stomach Mucosa	stomach
31	chr12:66615800-66618400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:66615800-66618800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:66616800-66626600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:66617600-66619800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:66618000-66618400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:66618000-66626600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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