Variant report

Variant	rs3802548
Chromosome Location	chr10:45952745-45952746
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:45946458-45953802	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45949197..45952104-chr10:45952176..45956457,4	K562	blood:
2	chr10:45948847..45950863-chr10:45951978..45954302,2	K562	blood:

Variant related genes	Relation type
ENSG00000231964	TF binding region

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10466245	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10900221	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10900223	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10900224	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10900229	0.83[ASN][1000 genomes]
rs10900230	0.83[ASN][1000 genomes]
rs10900232	0.83[ASN][1000 genomes]
rs11239528	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11239532	0.92[AFR][1000 genomes]
rs11239536	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11239538	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11239545	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11239549	0.93[EUR][1000 genomes]
rs11239551	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11239569	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11239571	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12242611	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12243153	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12246131	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12249012	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12257537	0.87[ASN][1000 genomes]
rs12257549	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12269403	0.87[ASN][1000 genomes]
rs2291428	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291429	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2310783	0.88[AFR][1000 genomes]
rs3891524	0.80[AFR][1000 genomes]
rs55665473	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56145077	0.84[AFR][1000 genomes]
rs58865519	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59390133	0.83[ASN][1000 genomes]
rs61854096	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61854123	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61854156	0.83[ASN][1000 genomes]
rs7076198	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7086046	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72796498	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs752059	0.89[AFR][1000 genomes]
rs970548	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv895107	chr10:45850300-45953767	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv895110	chr10:45912771-45953767	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription 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	2 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3802548	ALOX5	Cis_1M	lymphoblastoid	RTeQTL
rs3802548	FAM21A///FAM21B	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45938600-45967200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:45938600-45967200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:45942800-45953200	Weak transcription	Spleen	Spleen
4	chr10:45943000-45952800	Weak transcription	Primary B cells from cord blood	blood
5	chr10:45943200-45955000	Weak transcription	Colonic Mucosa	Colon
6	chr10:45943200-45965400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr10:45943400-45954000	Weak transcription	K562	blood
8	chr10:45946200-45954400	Weak transcription	Fetal Brain Female	brain
9	chr10:45947600-45952800	Weak transcription	Dnd41	blood
10	chr10:45947800-45953400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr10:45948000-45963600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr10:45948400-45955600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr10:45948600-45955600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:45948600-45959800	Strong transcription	Fetal Intestine Small	intestine
15	chr10:45948600-45959800	Strong transcription	Fetal Stomach	stomach
16	chr10:45948800-45953800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:45949200-45965600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr10:45949400-45954400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:45949400-45955400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr10:45949400-45959800	Strong transcription	Primary T cells from cord blood	blood
21	chr10:45949800-45953200	Weak transcription	Aorta	Aorta
22	chr10:45949800-45954200	Weak transcription	HSMMtube	muscle
23	chr10:45949800-45958600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr10:45950000-45952800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr10:45950000-45956800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr10:45950000-45967200	Weak transcription	Psoas Muscle	Psoas
27	chr10:45950200-45952800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:45950200-45959400	Strong transcription	Fetal Intestine Large	intestine
29	chr10:45950200-45960600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr10:45950400-45956800	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr10:45950400-45957000	Weak transcription	Fetal Kidney	kidney
32	chr10:45950400-45959400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:45950400-45959600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr10:45950400-45966200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr10:45950600-45953000	Weak transcription	Brain Angular Gyrus	brain
36	chr10:45950600-45953000	Weak transcription	Brain Substantia Nigra	brain
37	chr10:45950600-45953200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr10:45950600-45958600	Weak transcription	Right Atrium	heart
39	chr10:45950800-45952800	Weak transcription	Brain Anterior Caudate	brain
40	chr10:45950800-45953000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr10:45950800-45954800	Strong transcription	Brain Cingulate Gyrus	brain
42	chr10:45950800-45955400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:45950800-45955800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:45950800-45957000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr10:45950800-45965600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr10:45951000-45952800	Weak transcription	Brain Hippocampus Middle	brain
47	chr10:45951000-45953800	Strong transcription	Placenta	Placenta
48	chr10:45951000-45954200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr10:45951000-45955400	Strong transcription	Adipose Nuclei	Adipose
50	chr10:45951000-45955400	Strong transcription	Thymus	Thymus

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