Variant report

Variant	rs4278368
Chromosome Location	chr1:155722557-155722558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10908480	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10908481	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908482	0.99[ASN][1000 genomes]
rs11264409	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264410	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12024187	0.85[EUR][1000 genomes]
rs12035524	0.81[ASN][1000 genomes]
rs12040894	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12081192	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12407800	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12744132	0.81[ASN][1000 genomes]
rs2297775	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28582361	0.86[ASN][1000 genomes]
rs28662267	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2948071	0.86[ASN][1000 genomes]
rs2948072	0.87[ASN][1000 genomes]
rs2985707	0.90[ASN][1000 genomes]
rs348196	0.81[ASN][1000 genomes]
rs3738590	0.83[ASN][1000 genomes]
rs490608	0.94[ASN][1000 genomes]
rs6427286	0.97[ASN][1000 genomes]
rs6427287	0.98[ASN][1000 genomes]
rs6662953	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6665227	0.99[ASN][1000 genomes]
rs708611	0.93[ASN][1000 genomes]
rs7521594	0.83[ASN][1000 genomes]
rs7541060	0.98[ASN][1000 genomes]
rs7550402	0.98[ASN][1000 genomes]
rs821551	0.81[ASN][1000 genomes]
rs822025	0.87[ASN][1000 genomes]
rs822527	0.92[ASN][1000 genomes]
rs860295	0.83[ASN][1000 genomes]
rs9426933	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS 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	32 gene(s)	inside rSNPs	diseases
6	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
7	nsv3065	chr1:155682768-155727524	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4278368	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs4278368	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs4278368	RIT1	cis	Thyroid	GTEx
rs4278368	GON4L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155715400-155723000	Weak transcription	Aorta	Aorta
2	chr1:155715400-155725600	Weak transcription	Fetal Brain Male	brain
3	chr1:155715400-155726200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:155715400-155730000	Weak transcription	Stomach Mucosa	stomach
5	chr1:155715400-155739200	Weak transcription	Fetal Heart	heart
6	chr1:155715400-155789200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:155715600-155722800	Weak transcription	Fetal Kidney	kidney
8	chr1:155715600-155722800	Weak transcription	Gastric	stomach
9	chr1:155715600-155725000	Weak transcription	Small Intestine	intestine
10	chr1:155715600-155725200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:155715600-155725200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:155715600-155725400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:155715600-155726800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:155715600-155764600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:155716000-155722600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:155716000-155725000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:155716000-155793400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:155716200-155722800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:155716200-155722800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:155716200-155726800	Weak transcription	A549	lung
21	chr1:155716600-155725400	Strong transcription	Fetal Intestine Small	intestine
22	chr1:155716600-155781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:155717200-155725000	Strong transcription	Lung	lung
24	chr1:155717200-155725600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:155717200-155761000	Strong transcription	Fetal Stomach	stomach
26	chr1:155717400-155731000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:155717400-155733400	Strong transcription	Brain Anterior Caudate	brain
28	chr1:155717400-155795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:155717600-155733800	Strong transcription	Spleen	Spleen
30	chr1:155717600-155750200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:155718000-155729400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:155718200-155729400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:155718400-155722800	Weak transcription	GM12878-XiMat	blood
34	chr1:155718600-155722800	Weak transcription	Pancreas	Pancrea
35	chr1:155718800-155722800	Weak transcription	HMEC	breast
36	chr1:155718800-155726800	Weak transcription	Psoas Muscle	Psoas
37	chr1:155719000-155722600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:155719200-155722800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:155719200-155722800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:155719200-155723400	Weak transcription	NHDF-Ad	bronchial
41	chr1:155720000-155732000	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:155720200-155732800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:155720200-155732800	Strong transcription	Osteobl	bone
44	chr1:155720200-155733000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:155720200-155733800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:155720200-155745400	Strong transcription	Fetal Muscle Leg	muscle
47	chr1:155720200-155748600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:155720200-155748800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:155720200-155748800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:155720200-155749000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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