Variant report

Variant	rs10908481
Chromosome Location	chr1:155713650-155713651
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10908470	0.84[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs10908471	0.84[CEU][hapmap];0.91[JPT][hapmap]
rs10908479	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10908480	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10908482	1.00[ASN][1000 genomes]
rs11264380	0.84[CEU][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs11264381	0.84[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs11264387	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs11264409	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264410	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12024187	0.85[EUR][1000 genomes]
rs12035524	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.80[ASN][1000 genomes]
rs12040894	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12047756	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12081192	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12407800	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12744132	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1556488	0.84[CEU][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs2048431	0.88[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2175391	0.88[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs2282301	0.82[MEX][hapmap]
rs2297775	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2666826	1.00[JPT][hapmap]
rs28582361	0.86[ASN][1000 genomes]
rs28662267	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2948071	0.86[ASN][1000 genomes]
rs2948072	0.86[ASN][1000 genomes]
rs2985707	0.89[ASN][1000 genomes]
rs348196	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3738590	0.88[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs3820594	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3892792	0.84[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs4278368	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs475550	0.88[CEU][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs490608	0.95[ASN][1000 genomes]
rs6427286	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6427287	0.97[ASN][1000 genomes]
rs644853	0.91[JPT][hapmap]
rs6662953	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6665227	1.00[ASN][1000 genomes]
rs6667652	0.82[MEX][hapmap]
rs670876	0.85[CHB][hapmap]
rs678157	1.00[JPT][hapmap]
rs708611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs729022	0.87[MEX][hapmap]
rs7521594	0.82[ASN][1000 genomes]
rs7541060	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7550402	0.97[ASN][1000 genomes]
rs821551	0.90[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs822025	0.86[ASN][1000 genomes]
rs822478	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs822490	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs822508	0.87[MEX][hapmap]
rs822527	0.91[ASN][1000 genomes]
rs860295	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs867549	0.82[MEX][hapmap]
rs867550	0.82[MEX][hapmap]
rs9426933	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	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
7	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
8	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10908481	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs10908481	ROBLD3	cis	parietal	SCAN
rs10908481	YY1AP1	cis	parietal	SCAN
rs10908481	GPATCH4	cis	parietal	SCAN
rs10908481	GON4L	Cis_1M	lymphoblastoid	RTeQTL
rs10908481	RIT1	cis	Thyroid	GTEx
rs10908481	YY1AP1	cis	cerebellum	SCAN
rs10908481	SPRR3	cis	parietal	SCAN
rs10908481	PRUNE	cis	cerebellum	SCAN
rs10908481	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs10908481	RIT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155683200-155715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:155683800-155715000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:155687200-155715000	Weak transcription	Esophagus	oesophagus
4	chr1:155695600-155714600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:155695800-155714600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:155699000-155714800	Weak transcription	Stomach Mucosa	stomach
7	chr1:155701000-155714600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:155702000-155714600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:155704600-155714800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:155704600-155714800	Weak transcription	Fetal Lung	lung
11	chr1:155706800-155714800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:155707000-155714600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:155708000-155714400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:155708000-155714800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:155708200-155714200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:155708200-155714400	Weak transcription	Primary B cells from cord blood	blood
17	chr1:155708200-155714600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:155708200-155714600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:155708200-155714600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:155708200-155714600	Weak transcription	Brain Germinal Matrix	brain
21	chr1:155708200-155714600	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:155708200-155714600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:155708200-155714600	Weak transcription	Brain Substantia Nigra	brain
24	chr1:155708200-155714600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:155708200-155714600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:155708200-155714600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:155708200-155714600	Weak transcription	A549	lung
28	chr1:155708200-155714600	Weak transcription	K562	blood
29	chr1:155708200-155714600	Weak transcription	NHEK	skin
30	chr1:155708200-155714800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:155708200-155714800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:155708200-155714800	Weak transcription	Fetal Brain Male	brain
33	chr1:155708200-155714800	Weak transcription	Fetal Heart	heart
34	chr1:155708200-155715000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:155708200-155715000	Weak transcription	Gastric	stomach
36	chr1:155708400-155714600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:155708400-155714600	Weak transcription	Brain Angular Gyrus	brain
38	chr1:155708400-155714600	Weak transcription	HepG2	liver
39	chr1:155708400-155714800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:155708400-155714800	Weak transcription	Fetal Kidney	kidney
41	chr1:155708400-155714800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:155708400-155714800	Weak transcription	HUVEC	blood vessel
43	chr1:155708400-155714800	Weak transcription	NHDF-Ad	bronchial
44	chr1:155708600-155714400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:155708600-155714400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:155708600-155714400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:155708600-155714600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:155708600-155714600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:155708600-155714600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:155708600-155714600	Weak transcription	Muscle Satellite Cultured Cells	--

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