Variant report

Variant	rs2553809
Chromosome Location	chr11:35163486-35163487
allele	A/G
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	chr11:35162808-35163647	GM12891	blood:	n/a	n/a
2	MXI1	chr11:35163341-35163541	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:35159893-35163743	Hela-S3	cervix:	n/a	n/a
4	MXI1	chr11:35159789-35167151	IMR90	lung:	n/a	n/a
5	POLR2A	chr11:35162699-35163652	HL-60	blood:	n/a	n/a
6	POLR2A	chr11:35158320-35197578	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr11:35159386-35163856	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr11:35162626-35163737	GM12891	blood:	n/a	n/a
9	CHD1	chr11:35159647-35163874	IMR90	lung:	n/a	n/a
10	POLR2A	chr11:35159892-35169475	U87	brain:	n/a	n/a
11	POLR2A	chr11:35159882-35169364	GM12891	blood:	n/a	n/a
12	WRNIP1	chr11:35163118-35163639	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:35162930-35163713	GM12891	blood:	n/a	n/a
14	POLR2A	chr11:35160230-35163769	IMR90	lung:	n/a	n/a
15	POLR2A	chr11:35159950-35178999	U87	brain:	n/a	n/a
16	POLR2A	chr11:35160199-35163808	U87	brain:	n/a	n/a
17	POLR2A	chr11:35163138-35163636	HCT-116	colon:	n/a	n/a
18	POLR2A	chr11:35159686-35169512	GM12892	blood:	n/a	n/a
19	POLR2A	chr11:35162504-35163750	GM12892	blood:	n/a	n/a
20	POLR2A	chr11:35163214-35163670	GM12878	blood:	n/a	n/a
21	POLR2A	chr11:35163114-35163684	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:35159772-35163754	Hela-S3	cervix:	n/a	n/a
23	TCF7L2	chr11:35163030-35163546	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr11:35160329-35163508	MCF10A-Er-Src	breast:	n/a	n/a
25	MYC	chr11:35162896-35163493	NB4	blood:	n/a	chr11:35163313-35163323
26	POLR2A	chr11:35163089-35163746	HCT-116	colon:	n/a	n/a
27	POLR2A	chr11:35162471-35163572	GM12878	blood:	n/a	n/a
28	POLR2A	chr11:35159736-35164647	GM12892	blood:	n/a	n/a
29	POLR2A	chr11:35163107-35163544	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr11:35159692-35163784	GM12892	blood:	n/a	n/a
31	POLR2A	chr11:35160219-35163808	U87	brain:	n/a	n/a
32	SIN3AK20	chr11:35163060-35163699	PANC-1	pancreas:	n/a	n/a
33	SPI1	chr11:35162945-35163649	HL-60	blood:	n/a	chr11:35163422-35163435 chr11:35163260-35163273 chr11:35163263-35163270
34	POLR2A	chr11:35162144-35163703	GM12891	blood:	n/a	n/a
35	POLR2A	chr11:35163053-35163592	HL-60	blood:	n/a	n/a
36	MAX	chr11:35163119-35163602	NB4	blood:	n/a	chr11:35163313-35163323

No.	Distal block	Cell Line	Cell type
1	chr11:35163163..35167316-chr11:35171190..35174236,4	K562	blood:
2	chr11:35026967..35028548-chr11:35162664..35165084,2	MCF-7	breast:
3	chr11:35161963..35164830-chr11:35383993..35385550,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255521	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2553808	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2732571	0.83[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs353558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353625	0.80[CHB][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv540999	chr11:35021936-35185471	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv2758263	chr11:35029933-35226784	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv2759818	chr11:35029933-35238578	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv541000	chr11:35053717-35185471	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv541001	chr11:35053717-35224624	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2757437	chr11:35067482-35238578	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' 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 target site	27 gene(s)	inside rSNPs	diseases
8	esv2752912	chr11:35074167-35238578	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv508623	chr11:35094933-35203363	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv541002	chr11:35101282-35224624	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv541003	chr11:35122694-35261451	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	nsv541004	chr11:35122694-35297414	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2553809	CCDC73	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35159800-35163600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr11:35159800-35163600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr11:35159800-35165000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:35160000-35163600	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr11:35160200-35163600	Active TSS	Brain Substantia Nigra	brain
6	chr11:35160200-35165000	Active TSS	Rectal Smooth Muscle	rectum
7	chr11:35160200-35170200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:35160400-35164000	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr11:35160400-35164000	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr11:35160600-35164200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr11:35161200-35163600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr11:35161200-35163600	Flanking Active TSS	Dnd41	blood
13	chr11:35161200-35163800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:35161200-35163800	Flanking Active TSS	Fetal Thymus	thymus
15	chr11:35161200-35164200	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr11:35161200-35164600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:35161200-35165200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:35161200-35197400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
19	chr11:35161400-35163600	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr11:35161400-35163600	Transcr. at gene 5' and 3'	HMEC	breast
21	chr11:35161400-35163800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr11:35161400-35164000	Transcr. at gene 5' and 3'	NHEK	skin
23	chr11:35161400-35166000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:35161400-35166800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr11:35161600-35163600	Active TSS	Liver	Liver
26	chr11:35161600-35163600	Active TSS	Brain Angular Gyrus	brain
27	chr11:35161600-35163600	Active TSS	Brain Cingulate Gyrus	brain
28	chr11:35161600-35163600	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr11:35161600-35167400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr11:35161800-35163600	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr11:35161800-35163600	Active TSS	Right Atrium	heart
32	chr11:35161800-35164000	Active TSS	Adipose Nuclei	Adipose
33	chr11:35161800-35164200	Active TSS	Brain Hippocampus Middle	brain
34	chr11:35161800-35164200	Active TSS	Right Ventricle	heart
35	chr11:35161800-35165000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:35162000-35164400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr11:35162000-35165200	Weak transcription	Gastric	stomach
38	chr11:35162000-35169000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:35162000-35169000	Enhancers	Stomach Mucosa	stomach
40	chr11:35162200-35163600	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr11:35162200-35163600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr11:35162400-35163600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr11:35162400-35163800	Active TSS	Muscle Satellite Cultured Cells	--
44	chr11:35162400-35164000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:35162400-35164400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr11:35162600-35163600	Flanking Active TSS	Fetal Stomach	stomach
47	chr11:35162600-35164400	Flanking Active TSS	Osteobl	bone
48	chr11:35162600-35164600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:35162600-35164800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:35162600-35165400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin

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