Variant report

Variant	rs10896604
Chromosome Location	chr11:57085213-57085214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57059815..57061654-chr11:57084021..57086891,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10792086	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs10792088	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs10792089	0.92[ASN][1000 genomes]
rs10792091	1.00[ASN][1000 genomes]
rs10896598	1.00[ASN][1000 genomes]
rs10896603	0.92[ASN][1000 genomes]
rs10896605	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs10896608	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228991	0.81[EUR][1000 genomes]
rs11228995	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229003	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229011	1.00[ASN][1000 genomes]
rs11602265	0.92[ASN][1000 genomes]
rs11602266	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603691	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607950	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12361969	0.82[ASN][1000 genomes]
rs12365472	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576878	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs1815769	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2230649	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs34135716	0.92[ASN][1000 genomes]
rs4938863	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs4938864	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs61888886	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61888887	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61888888	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106462	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs7110052	1.00[CHD][hapmap]
rs7111339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951793	1.00[CHD][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv541048	chr11:57076815-57120781	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10896604	OR5M9	cis	cerebellum	SCAN
rs10896604	PRPF19	cis	cerebellum	SCAN
rs10896604	PDGFD	trans	lymphoblastoid	seeQTL
rs10896604	FAM46A	trans	lymphoblastoid	seeQTL
rs10896604	OR5B21	cis	cerebellum	SCAN
rs10896604	OR9G4	cis	parietal	SCAN
rs10896604	TIMM10	cis	parietal	SCAN
rs10896604	OR5R1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57079200-57091400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:57079400-57089600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:57079400-57091400	Weak transcription	Primary B cells from cord blood	blood
4	chr11:57079600-57086400	Genic enhancers	Gastric	stomach
5	chr11:57079600-57089400	Weak transcription	GM12878-XiMat	blood
6	chr11:57079600-57090800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:57079800-57085400	Strong transcription	Aorta	Aorta
8	chr11:57079800-57085400	Strong transcription	Fetal Brain Female	brain
9	chr11:57079800-57085600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
10	chr11:57079800-57086200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
11	chr11:57079800-57087400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:57079800-57088200	Genic enhancers	Pancreas	Pancrea
13	chr11:57079800-57089000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr11:57079800-57089400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:57079800-57090400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr11:57080000-57085400	Strong transcription	Brain Germinal Matrix	brain
17	chr11:57080000-57085400	Strong transcription	Brain Substantia Nigra	brain
18	chr11:57080000-57085600	Strong transcription	A549	lung
19	chr11:57080000-57085600	Strong transcription	Osteobl	bone
20	chr11:57080000-57088200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:57080200-57088800	Strong transcription	Dnd41	blood
22	chr11:57080400-57085400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:57080400-57085800	Strong transcription	NHDF-Ad	bronchial
24	chr11:57080400-57086400	Genic enhancers	Liver	Liver
25	chr11:57080600-57085600	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr11:57080600-57085800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:57081000-57085800	Strong transcription	HMEC	breast
28	chr11:57081000-57085800	Strong transcription	NHEK	skin
29	chr11:57081400-57085800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:57081600-57085600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:57082000-57086200	Genic enhancers	Duodenum Mucosa	Duodenum
32	chr11:57082000-57086800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:57082200-57085600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:57082200-57086600	Genic enhancers	Rectal Mucosa Donor 31	rectum
35	chr11:57082400-57086400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr11:57082400-57086800	Genic enhancers	Fetal Stomach	stomach
37	chr11:57082400-57087600	Genic enhancers	Fetal Muscle Leg	muscle
38	chr11:57082600-57085600	Genic enhancers	Fetal Kidney	kidney
39	chr11:57082600-57086200	Enhancers	Right Atrium	heart
40	chr11:57082800-57085800	Genic enhancers	NHLF	lung
41	chr11:57082800-57086400	Genic enhancers	Brain Hippocampus Middle	brain
42	chr11:57082800-57086800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
43	chr11:57082800-57088600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:57082800-57089200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:57082800-57089200	Genic enhancers	Placenta	Placenta
46	chr11:57083000-57085400	Weak transcription	Small Intestine	intestine
47	chr11:57083000-57086000	Genic enhancers	Left Ventricle	heart
48	chr11:57083000-57086200	Genic enhancers	Brain Inferior Temporal Lobe	brain
49	chr11:57083000-57086200	Genic enhancers	Colonic Mucosa	Colon
50	chr11:57083000-57086400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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