Variant report

Variant	rs2553808
Chromosome Location	chr11:35164108-35164109
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	WRNIP1	chr11:35164041-35164329	GM12878	blood:	n/a	n/a
2	CTCF	chr11:35164040-35164190	GM12801	blood:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
3	REST	chr11:35164090-35164541	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr11:35164100-35164250	BJ	skin:	n/a	chr11:35164102-35164112 chr11:35164105-35164114 chr11:35164101-35164114
5	CTCF	chr11:35163980-35164130	GM12872	blood:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
6	POLR2A	chr11:35163856-35164621	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr11:35164026-35164118	GM12891	blood:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
8	STAT3	chr11:35163997-35164530	MCF10A-Er-Src	breast:	n/a	n/a
9	REST	chr11:35164065-35164593	A549	lung:	n/a	n/a
10	POLR2A	chr11:35163904-35164636	Hela-S3	cervix:	n/a	n/a
11	MTA3	chr11:35163872-35164455	GM12878	blood:	n/a	n/a
12	SMC3	chr11:35163966-35164236	K562	blood:	n/a	chr11:35164101-35164115 chr11:35164101-35164111
13	CTCF	chr11:35164040-35164190	K562	blood:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
14	CTCF	chr11:35164060-35164210	GM06990	blood:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
15	CTCF	chr11:35164060-35164210	GM12864	blood:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
16	POLR2A	chr11:35164100-35164540	HUVEC	blood vessel:	n/a	n/a
17	RUNX3	chr11:35163949-35164321	GM12878	blood:	n/a	n/a
18	MAX	chr11:35163920-35164581	SK-N-SH	brain:	n/a	chr11:35164397-35164406
19	CTCF	chr11:35164000-35164150	HUVEC	blood vessel:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
20	FOSL1	chr11:35163919-35164711	HCT-116	colon:	n/a	chr11:35164395-35164407 chr11:35164398-35164409 chr11:35164396-35164406 chr11:35164397-35164405
21	POLR2A	chr11:35163875-35166323	GM12878	blood:	n/a	n/a
22	CEBPB	chr11:35163971-35164476	IMR90	lung:	n/a	n/a
23	MTA3	chr11:35163888-35164440	GM12878	blood:	n/a	n/a
24	MXI1	chr11:35159789-35167151	IMR90	lung:	n/a	n/a
25	RCOR1	chr11:35164013-35164254	GM12878	blood:	n/a	n/a
26	POLR2A	chr11:35163871-35166317	GM12892	blood:	n/a	n/a
27	CTCF	chr11:35164040-35164190	GM12871	blood:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
28	CTCF	chr11:35164010-35164192	GM12892	blood:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
29	CTCF	chr11:35164100-35164250	HCT-116	colon:	n/a	chr11:35164102-35164112 chr11:35164105-35164114 chr11:35164101-35164114
30	CTCF	chr11:35164010-35164202	SK-N-SH_RA	brain:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
31	MYC	chr11:35163982-35164310	MCF10A-Er-Src	breast:	n/a	n/a
32	CTCF	chr11:35164045-35164193	GM10266	blood:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
33	POLR2A	chr11:35163896-35164620	GM12891	blood:	n/a	n/a
34	POLR2A	chr11:35158320-35197578	PANC-1	pancreas:	n/a	n/a
35	CTCF	chr11:35164020-35164170	HVMF	connective:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
36	CTCF	chr11:35164040-35164190	MCF-7	breast:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
37	MXI1	chr11:35164087-35164287	GM12878	blood:	n/a	n/a
38	TEAD4	chr11:35163940-35164742	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr11:35163872-35164645	GM12891	blood:	n/a	n/a
40	CTCF	chr11:35164020-35164170	GM06990	blood:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
41	CTCF	chr11:35163960-35164230	WI-38	lung:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
42	FOSL2	chr11:35163975-35164702	SK-N-SH	brain:	n/a	chr11:35164395-35164407 chr11:35164398-35164409 chr11:35164396-35164406 chr11:35164397-35164405
43	EBF1	chr11:35163896-35164763	GM12878	blood:	n/a	n/a
44	CTCF	chr11:35164040-35164190	HFF-Myc	foreskin:	n/a	chr11:35164102-35164112 chr11:35164094-35164115 chr11:35164099-35164117 chr11:35164105-35164114 chr11:35164101-35164114
45	EP300	chr11:35163917-35164651	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr11:35163996-35164500	HCT-116	colon:	n/a	n/a
47	POLR2A	chr11:35159892-35169475	U87	brain:	n/a	n/a
48	RAD21	chr11:35163913-35164295	SK-N-SH_RA	brain:	n/a	chr11:35164101-35164111 chr11:35164099-35164111 chr11:35164097-35164116 chr11:35164101-35164115
49	RAD21	chr11:35164059-35164170	HepG2	liver:	n/a	chr11:35164101-35164111 chr11:35164099-35164111 chr11:35164097-35164116 chr11:35164101-35164115
50	POLR2A	chr11:35159882-35169364	GM12891	blood:	n/a	n/a

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:
4	chr11:34947697..34948269-chr11:35163627..35164578,3	K562	blood:

Variant related genes	Relation type
ENSG00000255521	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12272373	1.00[YRI][hapmap]
rs2553809	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];0.88[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs353558	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353625	0.80[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.88[ASN][1000 genomes]
rs353634	0.81[GIH][hapmap]
rs7111018	1.00[YRI][hapmap]

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
rs2553808	CCDC73	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35159800-35165000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:35160200-35165000	Active TSS	Rectal Smooth Muscle	rectum
3	chr11:35160200-35170200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:35160600-35164200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:35161200-35164200	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr11:35161200-35164600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:35161200-35165200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:35161200-35197400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
9	chr11:35161400-35166000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:35161400-35166800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr11:35161600-35167400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr11:35161800-35164200	Active TSS	Brain Hippocampus Middle	brain
13	chr11:35161800-35164200	Active TSS	Right Ventricle	heart
14	chr11:35161800-35165000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:35162000-35164400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr11:35162000-35165200	Weak transcription	Gastric	stomach
17	chr11:35162000-35169000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:35162000-35169000	Enhancers	Stomach Mucosa	stomach
19	chr11:35162400-35164400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr11:35162600-35164400	Flanking Active TSS	Osteobl	bone
21	chr11:35162600-35164600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:35162600-35164800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:35162600-35165400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:35162600-35165800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
25	chr11:35162800-35165400	Weak transcription	Brain Anterior Caudate	brain
26	chr11:35163000-35164800	Enhancers	Fetal Lung	lung
27	chr11:35163000-35165800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:35163000-35167400	Transcr. at gene 5' and 3'	NHLF	lung
29	chr11:35163000-35168000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:35163200-35164200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr11:35163200-35165600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:35163200-35168200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
33	chr11:35163200-35169800	Enhancers	Small Intestine	intestine
34	chr11:35163400-35164800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:35163400-35165000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr11:35163400-35165200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:35163400-35165400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:35163400-35166000	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
39	chr11:35163400-35166200	Transcr. at gene 5' and 3'	Hela-S3	cervix
40	chr11:35163400-35166600	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr11:35163400-35166600	Enhancers	HUVEC	blood vessel
42	chr11:35163400-35168200	Enhancers	HSMMtube	muscle
43	chr11:35163400-35173000	Weak transcription	Left Ventricle	heart
44	chr11:35163400-35178400	Weak transcription	Psoas Muscle	Psoas
45	chr11:35163600-35164200	Enhancers	Colonic Mucosa	Colon
46	chr11:35163600-35164200	Enhancers	Placenta	Placenta
47	chr11:35163600-35164200	Enhancers	Lung	lung
48	chr11:35163600-35164200	Enhancers	Dnd41	blood
49	chr11:35163600-35164400	Enhancers	Fetal Stomach	stomach
50	chr11:35163600-35164800	Weak transcription	Aorta	Aorta

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