Variant report

Variant	rs6486061
Chromosome Location	chr11:9024867-9024868
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	SIN3A	chr11:9024856-9025708	H1-hESC	embryonic stem cell:	n/a	chr11:9025194-9025207
2	UBTF	chr11:9024724-9025712	K562	blood:	n/a	n/a
3	MAZ	chr11:9024165-9026232	IMR90	lung:	n/a	chr11:9026108-9026121 chr11:9026109-9026120 chr11:9026110-9026119 chr11:9026110-9026119
4	MAX	chr11:9024576-9025381	NB4	blood:	n/a	n/a
5	ZNF263	chr11:9024405-9025735	HEK293-T-REx	kidney:	n/a	chr11:9025081-9025102 chr11:9024670-9024679 chr11:9025080-9025089
6	NR2F2	chr11:9024690-9025230	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:9022966..9025427-chr11:9154942..9157918,2	K562	blood:
2	chr11:8984349..8987280-chr11:9024480..9026486,3	K562	blood:
3	chr11:9023701..9026254-chr11:9404770..9407613,2	K562	blood:
4	chr11:9023067..9025427-chr11:9156418..9158861,2	K562	blood:
5	chr11:8996724..8999605-chr11:9022687..9025353,2	K562	blood:
6	chr11:8930312..8933119-chr11:9023959..9026944,2	K562	blood:
7	chr11:8930312..8934560-chr11:9023959..9026944,3	K562	blood:
8	chr11:8704228..8705954-chr11:9023702..9025627,2	K562	blood:

Variant related genes	Relation type
ENSG00000253973	TF binding region
ENSG00000254860	Chromatin interaction
ENSG00000200983	Chromatin interaction
ENSG00000175348	Chromatin interaction
ENSG00000205339	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000166444	Chromatin interaction
ENSG00000166452	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10734639	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs10769974	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs10840151	0.87[CHD][hapmap];0.84[JPT][hapmap];0.80[TSI][hapmap]
rs10840154	0.92[JPT][hapmap]
rs1136966	0.86[MEX][hapmap]
rs12794962	0.90[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs12805109	0.83[AMR][1000 genomes]
rs2568047	0.90[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs2653556	0.82[MEX][hapmap]
rs2653574	0.82[MEX][hapmap]
rs3751063	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs3751066	0.84[JPT][hapmap]
rs3751068	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs3763911	0.92[JPT][hapmap]
rs3763912	0.87[CHD][hapmap];0.84[JPT][hapmap];0.80[TSI][hapmap]
rs4370967	0.90[CEU][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs4909951	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs4910290	0.84[ASN][1000 genomes]
rs66630602	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7125458	0.82[MEX][hapmap]
rs7936201	0.82[MEX][hapmap]
rs9300096	0.87[CHD][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	esv3354735	chr11:9024401-9026949	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6486061	C11orf17	cis	lymphoblastoid	seeQTL
rs6486061	TMEM9B	cis	parietal	SCAN
rs6486061	C11orf17	cis	cerebellum	SCAN
rs6486061	NRIP3	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9023200-9025000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:9023800-9026600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr11:9024200-9025000	Flanking Active TSS	NHLF	lung
4	chr11:9024400-9025000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
5	chr11:9024400-9025000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:9024400-9025000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
7	chr11:9024400-9025000	Bivalent Enhancer	Liver	Liver
8	chr11:9024400-9025000	Flanking Active TSS	NHDF-Ad	bronchial
9	chr11:9024400-9025200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
10	chr11:9024400-9025200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
11	chr11:9024400-9025200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
12	chr11:9024400-9025200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:9024400-9025200	Flanking Active TSS	K562	blood
14	chr11:9024400-9025400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
15	chr11:9024400-9025400	Flanking Active TSS	Osteobl	bone
16	chr11:9024400-9025600	Flanking Active TSS	NH-A	brain
17	chr11:9024400-9026200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr11:9024400-9026600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr11:9024600-9025000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:9024600-9025000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:9024600-9025000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr11:9024600-9025000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr11:9024600-9025000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
24	chr11:9024600-9025000	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
25	chr11:9024600-9025000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
26	chr11:9024600-9025000	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:9024600-9025000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr11:9024600-9025000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:9024600-9025000	Enhancers	Aorta	Aorta
30	chr11:9024600-9025000	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
31	chr11:9024600-9025000	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
32	chr11:9024600-9025000	Bivalent Enhancer	Brain Substantia Nigra	brain
33	chr11:9024600-9025000	Bivalent Enhancer	Colonic Mucosa	Colon
34	chr11:9024600-9025000	Bivalent Enhancer	Placenta	Placenta
35	chr11:9024600-9025000	Enhancers	Left Ventricle	heart
36	chr11:9024600-9025000	Bivalent Enhancer	HepG2	liver
37	chr11:9024600-9025000	Flanking Active TSS	HSMM	muscle
38	chr11:9024600-9025200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:9024600-9025200	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
40	chr11:9024600-9025200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:9024600-9025200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:9024600-9025200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
43	chr11:9024600-9025200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
44	chr11:9024600-9025200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:9024600-9025200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
46	chr11:9024600-9025200	Enhancers	Gastric	stomach
47	chr11:9024600-9025200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
48	chr11:9024600-9025200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
49	chr11:9024600-9025200	Enhancers	Spleen	Spleen
50	chr11:9024600-9025200	Flanking Bivalent TSS/Enh	A549	lung

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