Variant report

Variant	rs11038741
Chromosome Location	chr11:5715184-5715185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:5715142-5716694	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:5715153-5715450	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr11:5715078-5715391	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:5714960-5715418	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	11:5033143-5038367..11:5714465-5718134	Hela-S3	cervix:
2	11:5349791-5355747..11:5714465-5718134	GM12878	blood:
3	11:4988858-5002113..11:5714465-5718134	Hela-S3	cervix:

Variant related genes	Relation type
TRIM22	TF binding region
ENSG00000225003	Chromatin interaction
ENSG00000236359	Chromatin interaction
ENSG00000224300	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10838534	0.81[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs11038751	0.81[ASN][1000 genomes]
rs1498555	0.84[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs17397821	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6578678	0.85[ASN][1000 genomes]
rs6578679	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7112085	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7129909	0.84[CEU][hapmap];0.89[CHB][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	nsv896949	chr11:5711177-5722444	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers 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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11038741	SNORA23	cis	cerebellum	SCAN
rs11038741	OR52W1	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5711600-5717800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:5711800-5717400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:5712000-5723000	Weak transcription	Fetal Stomach	stomach
4	chr11:5712200-5717800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:5712200-5719400	Weak transcription	Gastric	stomach
6	chr11:5712200-5723600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:5712200-5725200	Weak transcription	Fetal Heart	heart
8	chr11:5712400-5717000	Weak transcription	Aorta	Aorta
9	chr11:5712400-5717400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:5712400-5717400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:5712400-5717600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:5712400-5719400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:5712400-5723000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:5712400-5723000	Weak transcription	Fetal Intestine Large	intestine
15	chr11:5712400-5730200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:5712400-5730600	Weak transcription	Fetal Lung	lung
17	chr11:5712400-5731800	Weak transcription	NH-A	brain
18	chr11:5712400-5732400	Weak transcription	Pancreas	Pancrea
19	chr11:5712400-5732400	Weak transcription	Stomach Mucosa	stomach
20	chr11:5712600-5715600	Weak transcription	Ovary	ovary
21	chr11:5712600-5717400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:5712600-5717400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:5712600-5717400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr11:5712600-5717800	Weak transcription	Placenta	Placenta
25	chr11:5712600-5723800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:5712600-5729200	Weak transcription	Esophagus	oesophagus
27	chr11:5712600-5730200	Weak transcription	NHEK	skin
28	chr11:5712600-5732000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:5712600-5732600	Weak transcription	Colonic Mucosa	Colon
30	chr11:5713000-5716400	Weak transcription	HSMMtube	muscle
31	chr11:5713000-5717400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr11:5713000-5717400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:5713000-5717400	Weak transcription	Lung	lung
34	chr11:5713000-5717400	Weak transcription	HMEC	breast
35	chr11:5713000-5723000	Weak transcription	Right Ventricle	heart
36	chr11:5713000-5726000	Weak transcription	Left Ventricle	heart
37	chr11:5713000-5734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:5713200-5715200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:5713200-5717400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:5713200-5717600	Weak transcription	Fetal Muscle Leg	muscle
41	chr11:5713400-5717400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr11:5713400-5717400	Weak transcription	Liver	Liver
43	chr11:5713400-5717400	Weak transcription	Fetal Thymus	thymus
44	chr11:5713400-5717400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr11:5713600-5715400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr11:5713600-5716000	Weak transcription	NHDF-Ad	bronchial
47	chr11:5713600-5717400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr11:5713600-5717400	Weak transcription	HUVEC	blood vessel
49	chr11:5713600-5730800	Weak transcription	Brain Anterior Caudate	brain
50	chr11:5713600-5734800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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