Variant report

Variant	rs2296692
Chromosome Location	chr10:97373966-97373967
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1053905	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]
rs10786226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882638	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882640	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882641	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882642	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882643	0.85[CHB][hapmap]
rs10882644	0.85[CHB][hapmap]
rs10882649	0.85[CHB][hapmap]
rs10882654	1.00[CHB][hapmap]
rs11188397	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];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188398	0.85[CHB][hapmap]
rs11188399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188407	0.85[CHB][hapmap]
rs11188411	0.85[CHB][hapmap]
rs11188417	0.85[CHB][hapmap]
rs11188444	0.82[CHB][hapmap]
rs12778814	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12780161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409709	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461546	0.85[CHB][hapmap]
rs2296689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296691	0.85[CHB][hapmap]
rs4037	0.85[CHB][hapmap]
rs4258314	0.85[CHB][hapmap]
rs568046	0.81[ASW][hapmap]
rs58419111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100377	0.86[CHB][hapmap];0.85[TSI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs749050	0.85[CHB][hapmap]
rs7905711	0.85[ASN][1000 genomes]
rs943342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943343	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2296692	ALDH18A1	cis	cerebellum	SCAN
rs2296692	ENTPD1	cis	lymphoblastoid	seeQTL
rs2296692	C10orf12	cis	cerebellum	SCAN
rs2296692	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL

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	chr10:97364400-97378600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:97364400-97378600	Strong transcription	Fetal Brain Female	brain
6	chr10:97364400-97378600	Strong transcription	Spleen	Spleen
7	chr10:97364400-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr10:97364400-97403200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:97364600-97377400	Strong transcription	Placenta	Placenta
10	chr10:97364600-97378600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr10:97364600-97378600	Strong transcription	Pancreas	Pancrea
12	chr10:97364600-97378800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr10:97364600-97378800	Strong transcription	NH-A	brain
14	chr10:97364600-97379000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:97364600-97379000	Strong transcription	GM12878-XiMat	blood
16	chr10:97364600-97388400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr10:97364800-97378600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr10:97364800-97378600	Strong transcription	Gastric	stomach
19	chr10:97364800-97378800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:97364800-97378800	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr10:97364800-97378800	Strong transcription	Osteobl	bone
22	chr10:97364800-97379000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr10:97364800-97403400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr10:97364800-97411000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:97365000-97378200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:97365000-97378400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr10:97365000-97378600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:97365000-97378600	Strong transcription	Brain Germinal Matrix	brain
29	chr10:97365000-97378800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:97365000-97378800	Strong transcription	Adipose Nuclei	Adipose
31	chr10:97365000-97379000	Strong transcription	Dnd41	blood
32	chr10:97365000-97403000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr10:97365000-97403400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:97365200-97377800	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr10:97365200-97378600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr10:97365200-97378800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr10:97365200-97378800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr10:97365200-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:97365200-97379200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr10:97365200-97379200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr10:97365200-97379800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:97365200-97382200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr10:97365400-97376000	Strong transcription	Fetal Thymus	thymus
44	chr10:97365400-97377000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr10:97365400-97378600	Strong transcription	Lung	lung
46	chr10:97365400-97378800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr10:97365400-97378800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr10:97365400-97378800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr10:97365400-97378800	Strong transcription	NHEK	skin
50	chr10:97365400-97379000	Strong transcription	Fetal Muscle Trunk	muscle

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