Variant report

Variant	rs10900223
Chromosome Location	chr10:46021631-46021632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:46018607..46021116-chr10:46021525..46024218,2	K562	blood:
2	chr10:46017813..46021385-chr10:46021525..46026200,4	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10466245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793620	0.84[CEU][hapmap]
rs10900221	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900224	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900229	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900230	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900232	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239528	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239536	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239538	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239541	0.80[CEU][hapmap]
rs11239545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239549	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11239550	0.84[CEU][hapmap]
rs11239551	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239569	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239571	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242611	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12243153	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246131	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249012	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12257549	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12269403	0.96[ASN][1000 genomes]
rs2291428	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291429	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2310783	0.80[YRI][hapmap]
rs3802548	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55665473	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58865519	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59390133	0.93[ASN][1000 genomes]
rs61854096	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854123	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854156	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7076198	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72796498	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1043536	chr10:45915941-46076235	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv895111	chr10:45989745-46071900	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv1041417	chr10:46021181-46088061	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10900223	ALOX5	Cis_1M	lymphoblastoid	RTeQTL
rs10900223	FAM21A///FAM21B	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45999000-46025600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:46005000-46025200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr10:46005400-46029800	Weak transcription	Fetal Kidney	kidney
4	chr10:46007800-46027400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:46008400-46027200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr10:46008800-46021800	Weak transcription	Spleen	Spleen
7	chr10:46009400-46044400	Weak transcription	Thymus	Thymus
8	chr10:46010000-46027800	Weak transcription	Lung	lung
9	chr10:46010000-46056000	Weak transcription	Esophagus	oesophagus
10	chr10:46010200-46027200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:46010200-46028800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:46010800-46025600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr10:46011000-46025400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr10:46011400-46027200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:46011600-46030200	Weak transcription	HepG2	liver
16	chr10:46013200-46027400	Weak transcription	Left Ventricle	heart
17	chr10:46014000-46027400	Weak transcription	Fetal Intestine Small	intestine
18	chr10:46014400-46070000	Weak transcription	Psoas Muscle	Psoas
19	chr10:46015000-46025600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr10:46015400-46025800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr10:46015600-46026000	Weak transcription	Aorta	Aorta
22	chr10:46015600-46043400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr10:46016000-46022800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr10:46016000-46027400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr10:46016200-46027400	Weak transcription	Liver	Liver
26	chr10:46017200-46027000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:46017800-46027200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr10:46017800-46029600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr10:46018000-46052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr10:46018400-46027200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr10:46018400-46040400	Weak transcription	K562	blood
32	chr10:46018800-46027600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr10:46019200-46022000	Strong transcription	Primary T cells from cord blood	blood
34	chr10:46019200-46039200	Weak transcription	Fetal Intestine Large	intestine
35	chr10:46019800-46021800	Strong transcription	Primary B cells from cord blood	blood
36	chr10:46021000-46022000	Enhancers	Fetal Lung	lung
37	chr10:46021200-46028000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr10:46021400-46028000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr10:46021600-46021800	Enhancers	Brain Germinal Matrix	brain
40	chr10:46021600-46022000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr10:46021600-46022000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:46021600-46022000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr10:46021600-46022000	Enhancers	Brain Angular Gyrus	brain
44	chr10:46021600-46022000	Enhancers	Brain Hippocampus Middle	brain
45	chr10:46021600-46022000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr10:46021600-46022000	Enhancers	Fetal Muscle Trunk	muscle
47	chr10:46021600-46022000	Enhancers	Fetal Stomach	stomach
48	chr10:46021600-46022000	Enhancers	Gastric	stomach
49	chr10:46021600-46022000	Enhancers	Ovary	ovary
50	chr10:46021600-46022000	Enhancers	Pancreas	Pancrea

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