Variant report

Variant	rs11188404
Chromosome Location	chr10:97379226-97379227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10882643	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882644	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882649	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10882650	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188393	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11188394	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188396	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11188398	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188400	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188406	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188407	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188411	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188417	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11591779	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11592213	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357173	0.83[AFR][1000 genomes]
rs12359272	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17461546	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2004611	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017218	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2152916	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2296691	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763707	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4037	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258314	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417206	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4917697	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918951	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918955	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56322409	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57347444	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61871790	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61871792	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61871793	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61871796	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6946	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7072953	0.83[AFR][1000 genomes]
rs7073010	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs749050	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7917792	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8758	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11188404	ALDH18A1	Cis_1M	lymphoblastoid	RTeQTL
rs11188404	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	chr10:97364400-97403200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr10:97364600-97388400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr10:97364800-97403400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr10:97364800-97411000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:97365000-97403000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr10:97365000-97403400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr10:97365200-97379800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:97365200-97382200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr10:97365600-97380800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:97365800-97385000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:97367400-97388600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr10:97367600-97388400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr10:97368400-97393000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr10:97369600-97382200	Strong transcription	Primary hematopoietic stem cells	blood
18	chr10:97373800-97386600	Weak transcription	Fetal Brain Male	brain
19	chr10:97374000-97380800	Weak transcription	Stomach Mucosa	stomach
20	chr10:97374000-97386400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr10:97374400-97386600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr10:97375400-97387000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr10:97376200-97384400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:97376200-97400600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr10:97376400-97411400	Weak transcription	Psoas Muscle	Psoas
26	chr10:97376400-97415200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr10:97376600-97384800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr10:97376600-97385800	Weak transcription	Fetal Kidney	kidney
29	chr10:97376600-97415000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr10:97377400-97383400	Weak transcription	Small Intestine	intestine
31	chr10:97377800-97380200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr10:97377800-97380800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:97377800-97384600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr10:97378000-97380800	Weak transcription	Esophagus	oesophagus
35	chr10:97378000-97384000	Weak transcription	Colonic Mucosa	Colon
36	chr10:97378000-97384600	Weak transcription	Right Ventricle	heart
37	chr10:97378200-97380800	Weak transcription	Colon Smooth Muscle	Colon
38	chr10:97378200-97385200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr10:97378200-97386400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr10:97378200-97387200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr10:97378200-97391800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr10:97378400-97380800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr10:97378600-97379800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:97378600-97379800	Weak transcription	Brain Angular Gyrus	brain
45	chr10:97378600-97380200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:97378600-97380600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr10:97378600-97380600	Weak transcription	Fetal Stomach	stomach
48	chr10:97378600-97380800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr10:97378600-97380800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:97378600-97380800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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