Variant report

Variant	rs11239535
Chromosome Location	chr10:45978387-45978388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45976905..45979805-chr10:45980072..45982025,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10466245	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs10793619	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10793620	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10900218	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10900219	0.95[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10900220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10900221	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs10900222	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239528	0.89[GIH][hapmap]
rs11239537	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239541	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239545	0.83[GIH][hapmap]
rs11239548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239550	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239571	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs11499089	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12249012	0.81[CEU][hapmap]
rs12265787	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12269352	0.92[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12767823	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1982796	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34563674	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57491883	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7086046	0.81[GIH][hapmap]
rs7089063	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7908745	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs963029	0.89[ASN][1000 genomes]
rs964686	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs970548	0.81[GIH][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11239535	ZNF32	cis	parietal	SCAN
rs11239535	ALOX5	cis	cerebellum	SCAN
rs11239535	ZNF485	cis	parietal	SCAN
rs11239535	OR13A1	cis	cerebellum	SCAN
rs11239535	ALOX5	cis	parietal	SCAN
rs11239535	MARCH8	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45966400-45979800	Weak transcription	Thymus	Thymus
2	chr10:45967600-45979200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr10:45967600-45979600	Weak transcription	Ovary	ovary
4	chr10:45967600-45983400	Weak transcription	Right Atrium	heart
5	chr10:45967800-45980200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:45967800-45985200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr10:45968000-45986000	Weak transcription	HepG2	liver
8	chr10:45969400-45983800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr10:45969600-45983400	Weak transcription	Liver	Liver
10	chr10:45969600-45983400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:45969800-45983400	Weak transcription	Pancreas	Pancrea
12	chr10:45970600-45983400	Weak transcription	Left Ventricle	heart
13	chr10:45970800-45983400	Weak transcription	Gastric	stomach
14	chr10:45971200-45979800	Weak transcription	Lung	lung
15	chr10:45971400-45983800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr10:45971600-45979200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr10:45972200-45988000	Weak transcription	Spleen	Spleen
18	chr10:45973200-45982800	Weak transcription	Aorta	Aorta
19	chr10:45973400-45983800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr10:45973600-45982800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:45973800-45979600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr10:45973800-45980400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr10:45974200-45978400	Weak transcription	Brain Hippocampus Middle	brain
24	chr10:45974600-45978400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:45974800-45983400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:45974800-45990600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr10:45975000-45983400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr10:45975000-45983400	Weak transcription	Psoas Muscle	Psoas
29	chr10:45975400-45983600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr10:45975600-45979800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr10:45975800-45983400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr10:45976000-45979600	Weak transcription	Fetal Stomach	stomach
33	chr10:45976000-45980000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr10:45976000-45982800	Weak transcription	K562	blood
35	chr10:45976200-45980200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr10:45976200-45980200	Weak transcription	Fetal Muscle Leg	muscle
37	chr10:45976400-45982800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr10:45976400-45986000	Weak transcription	HSMMtube	muscle
39	chr10:45976600-45980200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr10:45976600-45980400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr10:45976800-45979600	Weak transcription	Primary T cells from cord blood	blood
42	chr10:45976800-45979800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr10:45977000-45979600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr10:45977000-45979800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr10:45977000-45980200	Weak transcription	Fetal Intestine Small	intestine
46	chr10:45977000-45984400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr10:45977200-45985600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr10:45977400-45980000	Weak transcription	Fetal Brain Female	brain
49	chr10:45977400-45982800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr10:45977600-45979800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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