Variant report

Variant	rs10908480
Chromosome Location	chr1:155699762-155699763
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155699238..155701661-chr1:155707272..155709440,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10908481	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10908482	0.84[ASN][1000 genomes]
rs11264409	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11264410	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12040894	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12081192	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12407800	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2297775	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28662267	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4278368	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs490608	0.88[ASN][1000 genomes]
rs6427286	0.83[ASN][1000 genomes]
rs6427287	0.84[ASN][1000 genomes]
rs6662953	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6665227	0.84[ASN][1000 genomes]
rs7541060	0.84[ASN][1000 genomes]
rs7550402	0.84[ASN][1000 genomes]
rs9426933	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	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
5	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv947547	chr1:155698814-155708436	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10908480	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs10908480	GON4L	Cis_1M	lymphoblastoid	RTeQTL
rs10908480	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs10908480	RIT1	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155660400-155706200	Weak transcription	Colonic Mucosa	Colon
2	chr1:155661600-155707800	Weak transcription	HUVEC	blood vessel
3	chr1:155663200-155701000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:155665200-155708000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:155665600-155707200	Weak transcription	Psoas Muscle	Psoas
6	chr1:155665800-155707000	Weak transcription	Small Intestine	intestine
7	chr1:155669200-155702200	Weak transcription	Gastric	stomach
8	chr1:155673800-155707800	Weak transcription	Aorta	Aorta
9	chr1:155676400-155706200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:155677400-155705200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:155679400-155710400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:155679800-155704200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:155681600-155707800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:155683000-155703200	Weak transcription	Spleen	Spleen
15	chr1:155683200-155715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:155683400-155707800	Weak transcription	Fetal Heart	heart
17	chr1:155683800-155709000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:155683800-155715000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:155684000-155700000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:155684000-155707800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:155685200-155704800	Strong transcription	Fetal Thymus	thymus
22	chr1:155687200-155715000	Weak transcription	Esophagus	oesophagus
23	chr1:155688400-155705000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:155688400-155711200	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:155688800-155710800	Strong transcription	Fetal Stomach	stomach
26	chr1:155688800-155711000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:155689200-155706000	Weak transcription	Fetal Brain Male	brain
28	chr1:155689200-155709400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:155689800-155701400	Weak transcription	Brain Germinal Matrix	brain
30	chr1:155690200-155706200	Weak transcription	Lung	lung
31	chr1:155690600-155702800	Weak transcription	Fetal Lung	lung
32	chr1:155691000-155709000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:155691200-155704600	Strong transcription	Placenta	Placenta
34	chr1:155691200-155705200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:155691800-155706200	Weak transcription	NHDF-Ad	bronchial
36	chr1:155692000-155700200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:155692200-155706200	Weak transcription	Ovary	ovary
38	chr1:155693800-155704800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:155694000-155702600	Weak transcription	Thymus	Thymus
40	chr1:155694800-155700400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:155694800-155704400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:155694800-155704600	Strong transcription	Dnd41	blood
43	chr1:155694800-155704600	Strong transcription	Hela-S3	cervix
44	chr1:155694800-155705000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:155695000-155704400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:155695000-155704600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:155695000-155704600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:155695000-155704600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:155695000-155704800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:155695000-155705000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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