Variant report

Variant	rs11227560
Chromosome Location	chr11:66426638-66426639
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66426389..66429166-chr11:66432505..66434138,2	MCF-7	breast:
2	chr11:66420097..66424743-chr11:66425989..66430549,5	MCF-7	breast:
3	chr11:66425713..66427527-chr11:66434728..66436810,2	MCF-7	breast:
4	chr11:66414467..66416321-chr11:66424430..66427161,2	MCF-7	breast:
5	chr11:66405702..66407631-chr11:66424589..66426650,2	MCF-7	breast:
6	chr11:66404797..66406683-chr11:66423062..66426708,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258297	Chromatin interaction
ENSG00000173933	Chromatin interaction
ENSG00000173914	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11227532	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs11227539	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11227554	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs11227562	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11227570	1.00[ASN][1000 genomes]
rs11227574	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[ASN][1000 genomes]
rs12049897	0.99[ASN][1000 genomes]
rs12223171	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12225302	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2229456	1.00[JPT][hapmap]
rs2275998	1.00[JPT][hapmap]
rs2276136	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv518919	chr11:66409409-66468469	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11227560	CCS	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66407000-66434400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:66411800-66436200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr11:66411800-66436400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:66411800-66442800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:66412000-66434400	Strong transcription	Fetal Thymus	thymus
6	chr11:66412000-66438800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:66412800-66430600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:66412800-66435800	Strong transcription	Thymus	Thymus
9	chr11:66412800-66436800	Strong transcription	Fetal Intestine Small	intestine
10	chr11:66413000-66435800	Strong transcription	Fetal Muscle Leg	muscle
11	chr11:66413000-66436600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:66413000-66440400	Strong transcription	Fetal Stomach	stomach
13	chr11:66413000-66442600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:66413400-66438400	Strong transcription	Dnd41	blood
15	chr11:66413600-66438400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:66413800-66430400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:66414000-66427000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:66414400-66427200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:66414800-66427000	Weak transcription	Fetal Heart	heart
20	chr11:66414800-66432600	Weak transcription	Aorta	Aorta
21	chr11:66414800-66436000	Weak transcription	Right Ventricle	heart
22	chr11:66414800-66442600	Weak transcription	Small Intestine	intestine
23	chr11:66415000-66438800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:66415200-66432200	Weak transcription	Psoas Muscle	Psoas
25	chr11:66415200-66433400	Weak transcription	Brain Substantia Nigra	brain
26	chr11:66415400-66427000	Weak transcription	Stomach Mucosa	stomach
27	chr11:66417000-66426800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:66417000-66430200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:66417800-66428400	Weak transcription	HSMMtube	muscle
30	chr11:66417800-66428800	Weak transcription	Brain Anterior Caudate	brain
31	chr11:66417800-66432200	Weak transcription	Gastric	stomach
32	chr11:66417800-66436200	Weak transcription	Esophagus	oesophagus
33	chr11:66418000-66428400	Weak transcription	Colonic Mucosa	Colon
34	chr11:66418200-66432000	Weak transcription	Spleen	Spleen
35	chr11:66418800-66434800	Weak transcription	Fetal Brain Male	brain
36	chr11:66419400-66427000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr11:66419400-66432600	Weak transcription	Fetal Kidney	kidney
38	chr11:66420000-66438400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:66420400-66427600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:66420400-66429400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:66420600-66427000	Weak transcription	Hela-S3	cervix
42	chr11:66420600-66428400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:66420600-66428400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:66420600-66428400	Weak transcription	Left Ventricle	heart
45	chr11:66420600-66443800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr11:66420800-66426800	Weak transcription	Ovary	ovary
47	chr11:66420800-66427000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr11:66420800-66427000	Weak transcription	HMEC	breast
49	chr11:66420800-66427200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:66420800-66427200	Weak transcription	Rectal Smooth Muscle	rectum

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