Variant report

Variant	rs56410179
Chromosome Location	chr11:17006273-17006274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17000932..17002613-chr11:17006244..17008801,2	MCF-7	breast:
2	chr11:16997178..16999092-chr11:17003135..17008712,4	MCF-7	breast:
3	chr11:16997842..17006545-chr11:17033236..17037894,15	MCF-7	breast:
4	chr11:16999245..17001608-chr11:17002120..17006650,5	MCF-7	breast:
5	chr11:16981957..16983634-chr11:17005634..17007658,3	MCF-7	breast:
6	chr11:17001912..17011357-chr11:17032509..17037700,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166689	Chromatin interaction
ENSG00000184669	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs34207405	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs55749020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55903519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57165913	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6486338	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7103326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7116064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950504	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9783287	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv983149	chr11:17003386-17011615	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16992200-17007400	Weak transcription	Colonic Mucosa	Colon
2	chr11:16998000-17009000	Enhancers	Stomach Mucosa	stomach
3	chr11:16998000-17011800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:16998800-17007800	Genic enhancers	Fetal Intestine Small	intestine
5	chr11:17000600-17011800	Enhancers	Pancreas	Pancrea
6	chr11:17001400-17010600	Enhancers	Placenta	Placenta
7	chr11:17001800-17006600	Weak transcription	Liver	Liver
8	chr11:17003000-17009800	Enhancers	Brain Substantia Nigra	brain
9	chr11:17003600-17007800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:17003600-17009800	Enhancers	Brain Anterior Caudate	brain
11	chr11:17004000-17006400	Enhancers	Brain Cingulate Gyrus	brain
12	chr11:17004000-17007400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:17004000-17007600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:17004000-17008000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:17004000-17008200	Weak transcription	Adipose Nuclei	Adipose
16	chr11:17004000-17008200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:17004000-17008400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:17004200-17007200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:17004200-17007200	Weak transcription	Right Ventricle	heart
20	chr11:17004200-17007600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:17004200-17007600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:17004200-17008000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:17004200-17008000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr11:17004200-17011200	Weak transcription	Brain Germinal Matrix	brain
25	chr11:17004400-17006800	Enhancers	HepG2	liver
26	chr11:17004400-17007400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:17004400-17007600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:17004400-17007600	Weak transcription	GM12878-XiMat	blood
29	chr11:17004400-17007800	Weak transcription	Spleen	Spleen
30	chr11:17004600-17006400	Weak transcription	A549	lung
31	chr11:17004600-17006600	Weak transcription	Left Ventricle	heart
32	chr11:17004600-17007000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:17004600-17007600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:17004800-17006400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr11:17004800-17006800	Weak transcription	Fetal Lung	lung
36	chr11:17004800-17007400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr11:17004800-17008000	Weak transcription	Fetal Muscle Leg	muscle
38	chr11:17004800-17034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:17005000-17006800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:17005000-17007000	Weak transcription	Fetal Kidney	kidney
41	chr11:17005000-17007600	Weak transcription	Right Atrium	heart
42	chr11:17005000-17009400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:17005200-17006600	Weak transcription	Lung	lung
44	chr11:17005200-17007000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:17005400-17009000	Enhancers	Fetal Intestine Large	intestine
46	chr11:17005800-17012200	Enhancers	Gastric	stomach
47	chr11:17006000-17006800	Enhancers	Esophagus	oesophagus
48	chr11:17006000-17007000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr11:17006000-17007200	Enhancers	Duodenum Mucosa	Duodenum
50	chr11:17006000-17007400	Enhancers	Rectal Mucosa Donor 29	rectum

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