Variant report

Variant	rs12624346
Chromosome Location	chr20:16419245-16419246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10485553	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12624938	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12624939	1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs17671618	0.90[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17671977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17672161	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17740473	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1998085	0.90[CEU][hapmap]
rs2180472	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34122290	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34550969	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4814484	0.82[TSI][hapmap]
rs56329134	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6034476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111116	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61664184	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7262082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7263619	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7268027	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73898731	0.98[EUR][1000 genomes]
rs73898736	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73898746	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8118656	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8120353	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8121801	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8125188	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833931	chr20:16308276-16460596	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12624346	OTOR	cis	cerebellum	SCAN
rs12624346	C20orf12	cis	parietal	SCAN
rs12624346	CNTN5	trans	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16384000-16432600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr20:16392200-16453000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr20:16398200-16431000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:16400000-16440000	Weak transcription	NHEK	skin
5	chr20:16404800-16419800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:16404800-16425000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:16405400-16434600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr20:16405600-16431000	Weak transcription	Pancreas	Pancrea
9	chr20:16408000-16420200	Weak transcription	Primary B cells from cord blood	blood
10	chr20:16408400-16424400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr20:16408600-16419600	Weak transcription	Fetal Intestine Small	intestine
12	chr20:16408600-16439200	Weak transcription	Brain Hippocampus Middle	brain
13	chr20:16408800-16424600	Weak transcription	Small Intestine	intestine
14	chr20:16409000-16431200	Weak transcription	Aorta	Aorta
15	chr20:16409200-16439400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr20:16409200-16443600	Weak transcription	Gastric	stomach
17	chr20:16409600-16431000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr20:16409800-16419400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr20:16409800-16419600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr20:16410200-16419600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:16410200-16420000	Weak transcription	Fetal Intestine Large	intestine
22	chr20:16410200-16424400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr20:16410200-16437400	Weak transcription	Esophagus	oesophagus
24	chr20:16410200-16455800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr20:16410200-16473200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr20:16410400-16424600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr20:16410400-16431000	Weak transcription	Liver	Liver
28	chr20:16410600-16425200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr20:16410600-16455400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr20:16411000-16424400	Weak transcription	Adipose Nuclei	Adipose
31	chr20:16411200-16439200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr20:16411200-16440000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr20:16411200-16455200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr20:16411400-16419800	Weak transcription	Primary T cells from cord blood	blood
35	chr20:16414400-16424600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr20:16414800-16421000	Weak transcription	Fetal Brain Male	brain
37	chr20:16414800-16424400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr20:16414800-16443600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr20:16417000-16431000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr20:16418400-16419600	Enhancers	HSMMtube	muscle
41	chr20:16418400-16420400	Enhancers	Fetal Muscle Leg	muscle
42	chr20:16418600-16420200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr20:16419200-16420000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr20:16419200-16420200	Enhancers	Fetal Heart	heart
45	chr20:16419200-16420200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr20:16419200-16420400	Enhancers	Left Ventricle	heart
47	chr20:16419200-16420400	Enhancers	Psoas Muscle	Psoas
48	chr20:16419200-16421000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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