Variant report

Variant	rs3750700
Chromosome Location	chr10:97392993-97392994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10509687	0.85[CHB][hapmap]
rs10736093	0.89[JPT][hapmap]
rs10748634	0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs10748638	0.83[ASW][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.87[AFR][1000 genomes]
rs10748642	0.89[JPT][hapmap]
rs10748643	0.89[JPT][hapmap]
rs10748648	0.83[JPT][hapmap]
rs10786228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10786236	0.88[JPT][hapmap]
rs10882646	0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs10882647	0.90[JPT][hapmap]
rs10882651	0.95[JPT][hapmap]
rs10882652	0.95[JPT][hapmap]
rs10882656	0.89[JPT][hapmap]
rs10882657	0.89[JPT][hapmap]
rs10882660	0.89[JPT][hapmap]
rs10882664	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10882665	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10882675	0.84[JPT][hapmap]
rs11188414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188425	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11188486	0.89[JPT][hapmap]
rs11188497	0.87[JPT][hapmap]
rs11596004	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs12244124	0.90[JPT][hapmap]
rs12244559	0.95[JPT][hapmap]
rs1418709	0.89[JPT][hapmap]
rs17111041	0.85[CHB][hapmap]
rs1890186	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1933165	0.89[JPT][hapmap]
rs1933169	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs2153913	0.89[JPT][hapmap]
rs2211002	0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap]
rs2225893	0.85[CHB][hapmap]
rs2275273	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.98[ASN][1000 genomes]
rs2297788	0.95[JPT][hapmap]
rs2485643	0.82[ASN][1000 genomes]
rs2861147	0.89[JPT][hapmap]
rs2861148	0.87[JPT][hapmap]
rs2861149	0.94[JPT][hapmap]
rs2901873	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2986401	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs3176891	0.89[JPT][hapmap]
rs3750701	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3793748	0.85[CHB][hapmap]
rs3793749	0.90[JPT][hapmap]
rs3814159	0.89[JPT][hapmap]
rs3929900	0.94[JPT][hapmap]
rs3934409	0.89[JPT][hapmap]
rs3949478	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs4074424	0.89[JPT][hapmap]
rs4075310	0.94[JPT][hapmap]
rs4290159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4396219	0.89[JPT][hapmap]
rs4431963	0.89[JPT][hapmap]
rs4501930	0.85[CHB][hapmap]
rs4551688	0.89[JPT][hapmap]
rs4582902	0.89[JPT][hapmap]
rs4917699	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4918950	0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap]
rs4918962	0.89[JPT][hapmap]
rs4918964	0.84[CHB][hapmap]
rs496426	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap]
rs497331	0.85[CHB][hapmap]
rs499714	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5014871	0.89[JPT][hapmap]
rs501819	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs535449	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs571505	0.85[CHB][hapmap]
rs6584022	0.94[JPT][hapmap]
rs6584023	0.89[JPT][hapmap]
rs6584027	0.89[JPT][hapmap]
rs7071836	0.89[JPT][hapmap]
rs7086986	0.89[JPT][hapmap]
rs7092594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7095587	0.89[JPT][hapmap]
rs7096317	0.84[JPT][hapmap]
rs749049	0.86[MKK][hapmap]
rs7894648	0.95[JPT][hapmap]
rs7902190	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs7909569	0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7920801	0.93[JPT][hapmap]
rs945958	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs9663413	0.90[JPT][hapmap]
rs9787589	0.81[AFR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3750700	CYP2C19	cis	parietal	SCAN
rs3750700	ENTPD1	cis	lymphoblastoid	seeQTL
rs3750700	ENTPD1	cis	Lymphoblastoid	GTEx
rs3750700	FRAT1	cis	cerebellum	SCAN
rs3750700	ALDH18A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97364000-97409200	Strong transcription	Primary T cells from cord blood	blood
2	chr10:97364000-97411000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr10:97364400-97403200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:97364800-97403400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr10:97364800-97411000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:97365000-97403000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr10:97365000-97403400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:97368400-97393000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:97376200-97400600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr10:97376400-97411400	Weak transcription	Psoas Muscle	Psoas
11	chr10:97376400-97415200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:97376600-97415000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr10:97378600-97414200	Weak transcription	Fetal Heart	heart
14	chr10:97379800-97403200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:97380200-97399200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr10:97380200-97403200	Strong transcription	Fetal Muscle Leg	muscle
17	chr10:97380200-97403400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:97380200-97408800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr10:97380600-97403000	Strong transcription	NH-A	brain
20	chr10:97380600-97403200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:97380600-97403200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:97380600-97408000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:97380800-97409000	Strong transcription	Osteobl	bone
24	chr10:97381200-97403400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr10:97381400-97393000	Weak transcription	Thymus	Thymus
26	chr10:97381600-97403000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr10:97383000-97411200	Strong transcription	Placenta	Placenta
28	chr10:97383200-97403000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr10:97383400-97398800	Strong transcription	Dnd41	blood
30	chr10:97383400-97400200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr10:97383400-97403000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr10:97383800-97394800	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr10:97383800-97395400	Strong transcription	HSMMtube	muscle
34	chr10:97383800-97397000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr10:97383800-97403000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr10:97383800-97403000	Strong transcription	Fetal Brain Female	brain
37	chr10:97383800-97403200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr10:97383800-97403200	Strong transcription	GM12878-XiMat	blood
39	chr10:97383800-97409400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr10:97383800-97410200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr10:97384000-97397200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr10:97384000-97397400	Strong transcription	Adipose Nuclei	Adipose
43	chr10:97384000-97402800	Strong transcription	HSMM	muscle
44	chr10:97384000-97403000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr10:97384000-97403200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr10:97384000-97403200	Strong transcription	Liver	Liver
47	chr10:97384200-97397000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr10:97384200-97403000	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr10:97384400-97397200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr10:97384400-97402800	Strong transcription	HUVEC	blood vessel

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