Variant report

Variant	rs10838534
Chromosome Location	chr11:5707688-5707689
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	11:4988858-5002113..11:5707362-5712027	Hela-S3	cervix:
2	chr11:5523660..5528079-chr11:5704615..5707879,4	K562	blood:
3	chr11:5706176..5707758-chr11:5710825..5713115,2	K562	blood:

Variant related genes	Relation type
ENSG00000196565	Chromatin interaction
ENSG00000225003	Chromatin interaction
ENSG00000213931	Chromatin interaction
ENSG00000132274	Chromatin interaction
ENSG00000167355	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11038741	0.81[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs11038751	0.88[ASN][1000 genomes]
rs17397821	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs6578678	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6578679	0.83[CHB][hapmap]
rs7112085	0.83[CHB][hapmap]
rs7129909	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats 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	34 gene(s)	inside rSNPs	diseases
5	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
10	nsv896948	chr11:5701281-5719667	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10838534	OR52W1	cis	cerebellum	SCAN
rs10838534	OR52B2	cis	parietal	SCAN
rs10838534	SNORA23	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5706200-5710000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:5706200-5711000	Weak transcription	Gastric	stomach
3	chr11:5706400-5710000	Weak transcription	Aorta	Aorta
4	chr11:5706400-5710200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr11:5706400-5710200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:5706400-5711000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:5706400-5711000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:5706400-5711000	Weak transcription	Lung	lung
9	chr11:5706600-5709000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:5706600-5709400	Weak transcription	Small Intestine	intestine
11	chr11:5706600-5710000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:5706600-5710000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:5706600-5710000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:5706600-5710000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr11:5706600-5710000	Weak transcription	Thymus	Thymus
16	chr11:5706600-5710200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:5706600-5710200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:5706600-5710200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:5706600-5710200	Weak transcription	Fetal Kidney	kidney
20	chr11:5706600-5710200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:5706600-5710200	Weak transcription	NHDF-Ad	bronchial
22	chr11:5706600-5710200	Weak transcription	NHLF	lung
23	chr11:5706600-5710400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr11:5706600-5710800	Weak transcription	Fetal Brain Male	brain
25	chr11:5706600-5710800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:5706600-5711000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:5706600-5711000	Weak transcription	Brain Hippocampus Middle	brain
28	chr11:5706600-5711000	Weak transcription	Brain Substantia Nigra	brain
29	chr11:5706600-5711000	Weak transcription	Colonic Mucosa	Colon
30	chr11:5706600-5711000	Weak transcription	Fetal Heart	heart
31	chr11:5706800-5708400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:5706800-5709000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:5706800-5709200	Weak transcription	Primary B cells from cord blood	blood
34	chr11:5706800-5709200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr11:5706800-5709600	Weak transcription	Primary T cells from cord blood	blood
36	chr11:5706800-5709600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr11:5706800-5709600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr11:5706800-5709600	Weak transcription	GM12878-XiMat	blood
39	chr11:5706800-5709800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:5706800-5709800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:5706800-5710000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:5706800-5710000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr11:5706800-5710200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:5706800-5710200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:5706800-5710200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:5706800-5710200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:5706800-5710200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:5706800-5710200	Weak transcription	Adipose Nuclei	Adipose
49	chr11:5706800-5710200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr11:5706800-5710200	Weak transcription	Rectal Smooth Muscle	rectum

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