Variant report

Variant	rs11239528
Chromosome Location	chr10:45955036-45955037
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:45949197..45952068-chr10:45954957..45956623,2	K562	blood:
2	chr10:45949197..45952104-chr10:45952176..45956457,4	K562	blood:
3	chr10:45954826..45957000-chr10:45957415..45959546,2	K562	blood:

Variant related genes	Relation type
ENSG00000165406	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10466245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1051713	0.80[YRI][hapmap]
rs10900221	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900223	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]
rs10900224	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900229	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs10900230	0.87[ASN][1000 genomes]
rs10900232	0.87[ASN][1000 genomes]
rs11239532	0.82[ASW][hapmap];0.85[CHD][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11239535	0.89[GIH][hapmap]
rs11239536	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239538	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239545	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239549	0.93[EUR][1000 genomes]
rs11239551	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11239569	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12242611	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12243153	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12246131	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12249012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12257537	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12257549	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12269403	0.90[ASN][1000 genomes]
rs2291428	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291429	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2310783	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs3802548	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55665473	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56145077	0.83[AFR][1000 genomes]
rs58865519	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59390133	0.87[ASN][1000 genomes]
rs61854096	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61854123	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61854156	0.87[ASN][1000 genomes]
rs7076198	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7086046	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72796498	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs752059	0.88[AFR][1000 genomes]
rs970548	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11239528	ALOX5	cis	parietal	SCAN
rs11239528	OR13A1	cis	cerebellum	SCAN
rs11239528	FAM21A///FAM21B	N/A	lymphoblastoid	RTeQTL
rs11239528	ALOX5	Cis_1M	lymphoblastoid	RTeQTL
rs11239528	ALOX5	cis	cerebellum	SCAN
rs11239528	ZNF32	cis	parietal	SCAN
rs11239528	ZNF485	cis	parietal	SCAN

Chromatin state (count:104 , 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	chr10:45943200-45965400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:45948000-45963600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:45948400-45955600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:45948600-45955600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:45948600-45959800	Strong transcription	Fetal Intestine Small	intestine
8	chr10:45948600-45959800	Strong transcription	Fetal Stomach	stomach
9	chr10:45949200-45965600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:45949400-45955400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr10:45949400-45959800	Strong transcription	Primary T cells from cord blood	blood
12	chr10:45949800-45958600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:45950000-45956800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr10:45950000-45967200	Weak transcription	Psoas Muscle	Psoas
15	chr10:45950200-45959400	Strong transcription	Fetal Intestine Large	intestine
16	chr10:45950200-45960600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr10:45950400-45956800	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr10:45950400-45957000	Weak transcription	Fetal Kidney	kidney
19	chr10:45950400-45959400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:45950400-45959600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:45950400-45966200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:45950600-45958600	Weak transcription	Right Atrium	heart
23	chr10:45950800-45955400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr10:45950800-45955800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:45950800-45957000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:45950800-45965600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr10:45951000-45955400	Strong transcription	Adipose Nuclei	Adipose
28	chr10:45951000-45955400	Strong transcription	Thymus	Thymus
29	chr10:45951000-45956400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr10:45951000-45956800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr10:45951000-45958400	Weak transcription	Fetal Heart	heart
32	chr10:45951000-45958800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr10:45951000-45960600	Weak transcription	Fetal Brain Male	brain
34	chr10:45951000-45965600	Weak transcription	Brain Germinal Matrix	brain
35	chr10:45951200-45955200	Strong transcription	Gastric	stomach
36	chr10:45951200-45958600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr10:45951200-45959000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr10:45951200-45959400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr10:45951200-45959600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr10:45951200-45959600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr10:45951200-45960600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr10:45951400-45955600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr10:45951400-45962200	Weak transcription	HMEC	breast
44	chr10:45951600-45955200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr10:45951600-45955600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr10:45951600-45955600	Strong transcription	Pancreas	Pancrea
47	chr10:45951600-45956000	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr10:45951600-45956200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:45951600-45956800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:45951600-45957000	Strong transcription	Primary T helper cells PMA-I stimulated	--

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