Variant report

Variant	rs58865519
Chromosome Location	chr10:46010891-46010892
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:46010308..46013233-chr10:46016249..46018005,2	MCF-7	breast:
2	chr10:46009283..46010923-chr10:46013025..46015001,2	K562	blood:
3	chr10:46009283..46011028-chr10:46011723..46015001,3	K562	blood:

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

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

rs_ID	r²[population]
rs10466245	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900221	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900223	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900224	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900229	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900230	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900232	0.93[ASN][1000 genomes]
rs11239528	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239532	0.91[AFR][1000 genomes]
rs11239536	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239538	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239545	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239549	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11239551	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239569	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239571	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242611	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12243153	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246131	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249012	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257537	0.96[ASN][1000 genomes]
rs12257549	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12269403	0.96[ASN][1000 genomes]
rs2291428	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291429	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2310783	0.87[AFR][1000 genomes]
rs3802548	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55665473	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56145077	0.83[AFR][1000 genomes]
rs59390133	0.93[ASN][1000 genomes]
rs61854096	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854123	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854156	0.93[ASN][1000 genomes]
rs7076198	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086046	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72796498	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs752059	0.88[AFR][1000 genomes]
rs970548	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58865519	FAM21A///FAM21B	N/A	lymphoblastoid	RTeQTL
rs58865519	ALOX5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45984200-46011000	Weak transcription	Left Ventricle	heart
2	chr10:45989200-46015200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:45999000-46025600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr10:46000800-46019800	Weak transcription	Primary B cells from cord blood	blood
5	chr10:46005000-46025200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr10:46005400-46029800	Weak transcription	Fetal Kidney	kidney
7	chr10:46007600-46021600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr10:46007800-46027400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:46008400-46027200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr10:46008800-46011400	Enhancers	Fetal Brain Female	brain
11	chr10:46008800-46011600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:46008800-46011600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr10:46008800-46021800	Weak transcription	Spleen	Spleen
14	chr10:46009000-46011600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr10:46009000-46011600	Enhancers	HepG2	liver
16	chr10:46009000-46021000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr10:46009200-46015200	Weak transcription	Aorta	Aorta
18	chr10:46009400-46044400	Weak transcription	Thymus	Thymus
19	chr10:46009600-46011400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr10:46009600-46011400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:46009600-46011400	Enhancers	Pancreas	Pancrea
22	chr10:46009800-46011200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr10:46009800-46011200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr10:46009800-46011400	Enhancers	H1 Cell Line	embryonic stem cell
25	chr10:46010000-46011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr10:46010000-46011200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:46010000-46011200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr10:46010000-46011200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr10:46010000-46011400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr10:46010000-46011600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr10:46010000-46011600	Enhancers	Brain Germinal Matrix	brain
32	chr10:46010000-46012800	Weak transcription	Psoas Muscle	Psoas
33	chr10:46010000-46015000	Weak transcription	Ovary	ovary
34	chr10:46010000-46021600	Weak transcription	Right Atrium	heart
35	chr10:46010000-46027800	Weak transcription	Lung	lung
36	chr10:46010000-46056000	Weak transcription	Esophagus	oesophagus
37	chr10:46010200-46011000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr10:46010200-46011200	Enhancers	NHDF-Ad	bronchial
39	chr10:46010200-46011200	Enhancers	Osteobl	bone
40	chr10:46010200-46011400	Enhancers	Brain Angular Gyrus	brain
41	chr10:46010200-46011600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr10:46010200-46011600	Enhancers	Brain Anterior Caudate	brain
43	chr10:46010200-46011800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:46010200-46011800	Enhancers	Brain Hippocampus Middle	brain
45	chr10:46010200-46027200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:46010200-46028800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr10:46010400-46011000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr10:46010400-46011200	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr10:46010400-46011400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr10:46010400-46011400	Enhancers	Brain Inferior Temporal Lobe	brain

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