Variant report

Variant	rs535449
Chromosome Location	chr10:97378785-97378786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10748634	0.85[JPT][hapmap]
rs10748638	0.90[JPT][hapmap]
rs10748642	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10748643	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10786228	0.89[JPT][hapmap]
rs10786229	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10786236	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs10882645	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882646	0.85[JPT][hapmap]
rs10882647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882651	0.82[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882652	0.82[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10882656	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10882657	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10882660	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10882664	0.85[JPT][hapmap]
rs10882665	0.85[JPT][hapmap]
rs11188414	0.90[JPT][hapmap]
rs11188416	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188486	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs11188497	0.88[JPT][hapmap]
rs12244124	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12244559	0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12251664	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12267876	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1268608	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12783226	0.81[CEU][hapmap]
rs1418709	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1933165	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1933167	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1933169	0.83[JPT][hapmap]
rs2153913	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2185818	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs2211002	0.85[JPT][hapmap]
rs2275273	0.90[JPT][hapmap]
rs2297788	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2861147	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2861148	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs2861149	0.85[JPT][hapmap]
rs2986401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750700	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs3750701	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs3793749	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814159	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs3929900	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs3934409	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs3949478	0.85[JPT][hapmap]
rs4074424	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4075310	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4396219	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4431963	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4551688	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4582902	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4918950	0.85[JPT][hapmap]
rs4918962	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs496426	0.90[JPT][hapmap]
rs499714	0.81[ASN][1000 genomes]
rs5014871	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs501819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507017	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543672	0.86[ASN][1000 genomes]
rs6584013	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6584022	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6584023	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs6584027	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs7069943	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7071836	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs7075081	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7079312	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7086986	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs7095587	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs7096317	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7097074	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7894648	0.82[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7895976	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs7909569	0.85[JPT][hapmap]
rs7920801	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs945958	0.85[JPT][hapmap]
rs9663413	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs535449	ALDH18A1	cis	lymphoblastoid	seeQTL
rs535449	LGI1	cis	parietal	SCAN
rs535449	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL
rs535449	TCTN3	cis	lymphoblastoid	seeQTL
rs535449	ENTPD1	cis	multi-tissue	Pritchard
rs535449	ENTPD1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97364000-97382000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr10:97364000-97409200	Strong transcription	Primary T cells from cord blood	blood
3	chr10:97364000-97411000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:97364400-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr10:97364400-97403200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:97364600-97378800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr10:97364600-97378800	Strong transcription	NH-A	brain
8	chr10:97364600-97379000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:97364600-97379000	Strong transcription	GM12878-XiMat	blood
10	chr10:97364600-97388400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:97364800-97378800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:97364800-97378800	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr10:97364800-97378800	Strong transcription	Osteobl	bone
14	chr10:97364800-97379000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr10:97364800-97403400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr10:97364800-97411000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:97365000-97378800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:97365000-97378800	Strong transcription	Adipose Nuclei	Adipose
19	chr10:97365000-97379000	Strong transcription	Dnd41	blood
20	chr10:97365000-97403000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr10:97365000-97403400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr10:97365200-97378800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr10:97365200-97378800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr10:97365200-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr10:97365200-97379200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr10:97365200-97379200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:97365200-97379800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr10:97365200-97382200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr10:97365400-97378800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr10:97365400-97378800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr10:97365400-97378800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr10:97365400-97378800	Strong transcription	NHEK	skin
33	chr10:97365400-97379000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr10:97365600-97378800	Strong transcription	Fetal Muscle Leg	muscle
35	chr10:97365600-97380800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr10:97365800-97378800	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr10:97365800-97378800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr10:97365800-97385000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr10:97366000-97378800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr10:97366000-97378800	Strong transcription	Hela-S3	cervix
41	chr10:97366200-97378800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr10:97366400-97378800	Strong transcription	HUVEC	blood vessel
43	chr10:97366600-97378800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr10:97366600-97378800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr10:97366800-97378800	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr10:97366800-97378800	Strong transcription	HSMM	muscle
47	chr10:97367200-97378800	Strong transcription	NHLF	lung
48	chr10:97367200-97379000	Strong transcription	A549	lung
49	chr10:97367400-97378800	Strong transcription	HSMMtube	muscle
50	chr10:97367400-97388600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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