Variant report

Variant	rs12040894
Chromosome Location	chr1:155761508-155761509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10796954	0.83[ASN][1000 genomes]
rs10908480	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10908481	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10908482	0.86[ASN][1000 genomes]
rs11264409	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11264410	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264413	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12024187	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12024257	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12081192	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12407800	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1973768	0.85[ASN][1000 genomes]
rs2297775	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28582361	1.00[ASN][1000 genomes]
rs28662267	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2948071	0.93[ASN][1000 genomes]
rs2948072	0.94[ASN][1000 genomes]
rs2985707	0.96[ASN][1000 genomes]
rs35698157	0.80[ASN][1000 genomes]
rs4278368	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs490608	0.81[ASN][1000 genomes]
rs6427286	0.87[ASN][1000 genomes]
rs6427287	0.88[ASN][1000 genomes]
rs6657670	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6662953	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6665227	0.86[ASN][1000 genomes]
rs708611	0.93[ASN][1000 genomes]
rs7541060	0.88[ASN][1000 genomes]
rs7550402	0.88[ASN][1000 genomes]
rs822025	0.94[ASN][1000 genomes]
rs822527	0.92[ASN][1000 genomes]
rs860295	0.97[ASN][1000 genomes]
rs9426933	0.82[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	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872469	chr1:155743310-155810293	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12040894	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs12040894	RIT1	cis	Thyroid	GTEx
rs12040894	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12040894	GON4L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155715400-155789200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:155715600-155764600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:155716000-155793400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:155716600-155781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:155717400-155795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:155720200-155798200	Strong transcription	Fetal Thymus	thymus
7	chr1:155720200-155803600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:155720400-155796800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:155730400-155764200	Weak transcription	Psoas Muscle	Psoas
10	chr1:155732200-155789200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:155737200-155772200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:155743000-155763400	Weak transcription	HMEC	breast
13	chr1:155743200-155773400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:155743600-155762200	Weak transcription	NHDF-Ad	bronchial
15	chr1:155746400-155774000	Weak transcription	Pancreas	Pancrea
16	chr1:155746400-155791400	Weak transcription	Stomach Mucosa	stomach
17	chr1:155746600-155763400	Weak transcription	Spleen	Spleen
18	chr1:155747000-155763000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:155747000-155764200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:155747200-155763400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:155747400-155763200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:155747600-155764000	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:155747600-155764200	Weak transcription	A549	lung
24	chr1:155747600-155764400	Weak transcription	Ovary	ovary
25	chr1:155747600-155776200	Weak transcription	Right Ventricle	heart
26	chr1:155747600-155787200	Weak transcription	Esophagus	oesophagus
27	chr1:155747800-155762200	Weak transcription	K562	blood
28	chr1:155747800-155762600	Weak transcription	NHLF	lung
29	chr1:155747800-155764400	Weak transcription	NHEK	skin
30	chr1:155747800-155785600	Weak transcription	Fetal Brain Male	brain
31	chr1:155747800-155791200	Weak transcription	Fetal Heart	heart
32	chr1:155748000-155789400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:155748800-155771600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:155749800-155766400	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:155751800-155765600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:155751800-155777600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:155752000-155765800	Strong transcription	Adipose Nuclei	Adipose
38	chr1:155752000-155771000	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:155752200-155763600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:155752800-155762600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:155754800-155762800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:155754800-155770600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:155755000-155761800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:155755000-155761800	Weak transcription	Brain Anterior Caudate	brain
45	chr1:155755000-155762400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:155755000-155762600	Weak transcription	Left Ventricle	heart
47	chr1:155755000-155762800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:155755000-155763200	Weak transcription	Fetal Lung	lung
49	chr1:155755000-155772600	Weak transcription	Gastric	stomach
50	chr1:155755200-155762200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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