Variant report

Variant	rs11239551
Chromosome Location	chr10:46026107-46026108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10466245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900221	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900223	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900224	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900229	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10900230	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10900232	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11239528	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11239536	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11239538	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239545	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239549	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11239569	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239571	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12242611	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12243153	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12246131	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12249012	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12257537	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12257549	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12269403	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2291428	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291429	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3802548	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55665473	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58865519	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59390133	0.87[ASN][1000 genomes]
rs61854096	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61854123	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61854156	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7076198	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7086046	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72796498	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs970548	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv528750	chr10:46024620-46076235	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1052233	chr10:46024620-46088061	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS 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
rs11239551	FAM21A///FAM21B	N/A	lymphoblastoid	RTeQTL
rs11239551	ALOX5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46005400-46029800	Weak transcription	Fetal Kidney	kidney
2	chr10:46007800-46027400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:46008400-46027200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr10:46009400-46044400	Weak transcription	Thymus	Thymus
5	chr10:46010000-46027800	Weak transcription	Lung	lung
6	chr10:46010000-46056000	Weak transcription	Esophagus	oesophagus
7	chr10:46010200-46027200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr10:46010200-46028800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr10:46011400-46027200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:46011600-46030200	Weak transcription	HepG2	liver
11	chr10:46013200-46027400	Weak transcription	Left Ventricle	heart
12	chr10:46014000-46027400	Weak transcription	Fetal Intestine Small	intestine
13	chr10:46014400-46070000	Weak transcription	Psoas Muscle	Psoas
14	chr10:46015600-46043400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr10:46016000-46027400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr10:46016200-46027400	Weak transcription	Liver	Liver
17	chr10:46017200-46027000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:46017800-46027200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr10:46017800-46029600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr10:46018000-46052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr10:46018400-46027200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr10:46018400-46040400	Weak transcription	K562	blood
23	chr10:46018800-46027600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr10:46019200-46039200	Weak transcription	Fetal Intestine Large	intestine
25	chr10:46021200-46028000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr10:46021400-46028000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr10:46021800-46029400	Weak transcription	Brain Germinal Matrix	brain
28	chr10:46021800-46030200	Weak transcription	Primary B cells from cord blood	blood
29	chr10:46022000-46027000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:46022000-46027400	Weak transcription	Fetal Lung	lung
31	chr10:46022000-46027400	Weak transcription	Fetal Stomach	stomach
32	chr10:46022000-46027400	Weak transcription	Ovary	ovary
33	chr10:46022000-46027400	Weak transcription	Pancreas	Pancrea
34	chr10:46022000-46027400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr10:46022000-46027600	Weak transcription	Brain Hippocampus Middle	brain
36	chr10:46022000-46027800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:46022000-46028800	Weak transcription	Placenta	Placenta
38	chr10:46022000-46029800	Weak transcription	Primary T cells from cord blood	blood
39	chr10:46022000-46030200	Weak transcription	Gastric	stomach
40	chr10:46022000-46030400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr10:46022000-46032600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr10:46022000-46043400	Weak transcription	Brain Angular Gyrus	brain
43	chr10:46022000-46046600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr10:46022200-46027000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr10:46022200-46027000	Weak transcription	Adipose Nuclei	Adipose
46	chr10:46022200-46028000	Weak transcription	Fetal Muscle Leg	muscle
47	chr10:46022200-46029800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr10:46022200-46030000	Weak transcription	Brain Substantia Nigra	brain
49	chr10:46022200-46043600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr10:46022800-46030200	Weak transcription	Colon Smooth Muscle	Colon

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