Variant report

Variant	rs11239534
Chromosome Location	chr10:45968590-45968591
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45967645..45969992-chr9:132259614..132262437,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204054	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1051713	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs10900215	1.00[ASN][1000 genomes]
rs10900228	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239523	1.00[ASN][1000 genomes]
rs11239524	1.00[ASN][1000 genomes]
rs11239532	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs11239540	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239572	1.00[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355888	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2310783	0.82[EUR][1000 genomes]
rs28395868	1.00[ASN][1000 genomes]
rs28586924	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891524	0.82[EUR][1000 genomes]
rs56071381	1.00[ASN][1000 genomes]
rs56145077	0.82[EUR][1000 genomes]
rs61854113	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854124	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72796464	1.00[ASN][1000 genomes]
rs72796496	1.00[ASN][1000 genomes]
rs72798218	1.00[ASN][1000 genomes]
rs72798220	1.00[ASN][1000 genomes]
rs752059	0.82[EUR][1000 genomes]
rs7897036	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11239534	ALOX5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45953600-45969200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:45960200-45970000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:45960400-45968600	Enhancers	Primary hematopoietic stem cells	blood
4	chr10:45960400-45971000	Enhancers	Brain Cingulate Gyrus	brain
5	chr10:45964800-45971200	Weak transcription	Fetal Brain Male	brain
6	chr10:45965200-45970800	Enhancers	Brain Substantia Nigra	brain
7	chr10:45965400-45969200	Enhancers	Brain Anterior Caudate	brain
8	chr10:45965400-45970400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr10:45965600-45969400	Enhancers	Colon Smooth Muscle	Colon
10	chr10:45965600-45969600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr10:45965600-45970000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr10:45966000-45969800	Enhancers	Brain Angular Gyrus	brain
13	chr10:45966200-45968600	Weak transcription	Fetal Brain Female	brain
14	chr10:45966200-45969800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr10:45966200-45971600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr10:45966400-45969000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr10:45966400-45979800	Weak transcription	Thymus	Thymus
18	chr10:45966800-45970400	Weak transcription	Fetal Intestine Small	intestine
19	chr10:45967000-45970000	Enhancers	Brain Hippocampus Middle	brain
20	chr10:45967000-45971600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr10:45967200-45970200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr10:45967400-45968800	Enhancers	K562	blood
23	chr10:45967400-45971200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr10:45967400-45971600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr10:45967600-45968600	Weak transcription	Fetal Muscle Leg	muscle
26	chr10:45967600-45968800	Weak transcription	Gastric	stomach
27	chr10:45967600-45968800	Weak transcription	Right Ventricle	heart
28	chr10:45967600-45968800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr10:45967600-45968800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:45967600-45969000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr10:45967600-45969000	Weak transcription	Fetal Stomach	stomach
32	chr10:45967600-45969200	Weak transcription	Pancreas	Pancrea
33	chr10:45967600-45969600	Enhancers	Liver	Liver
34	chr10:45967600-45970200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr10:45967600-45970200	Weak transcription	Spleen	Spleen
36	chr10:45967600-45970400	Weak transcription	Lung	lung
37	chr10:45967600-45970600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr10:45967600-45971200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr10:45967600-45971800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr10:45967600-45972400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr10:45967600-45974800	Weak transcription	Psoas Muscle	Psoas
42	chr10:45967600-45979200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr10:45967600-45979600	Weak transcription	Ovary	ovary
44	chr10:45967600-45983400	Weak transcription	Right Atrium	heart
45	chr10:45967800-45968600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr10:45967800-45969000	Weak transcription	Adipose Nuclei	Adipose
47	chr10:45967800-45969200	Weak transcription	Left Ventricle	heart
48	chr10:45967800-45971000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr10:45967800-45980200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr10:45967800-45985200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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