Variant report

Variant	rs2553824
Chromosome Location	chr11:35103592-35103593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:35101233..35103768-chr11:35185557..35187275,2	MCF-7	breast:
2	chr11:35097231..35099674-chr11:35101240..35103980,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD44-5	chr11:35103203-35103622	NONHSAT018771

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11523460	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1365057	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2093663	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2248428	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2553818	0.84[AMR][1000 genomes]
rs2553822	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2553823	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732534	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732535	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2785188	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2785191	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs890239	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs890240	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv430371	chr11:34975067-35111292	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35097600-35103800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr11:35097600-35106400	Enhancers	Primary B cells from peripheral blood	blood
3	chr11:35097800-35106600	Enhancers	Fetal Thymus	thymus
4	chr11:35098800-35103600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr11:35098800-35103800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:35098800-35104000	Weak transcription	Psoas Muscle	Psoas
7	chr11:35098800-35104000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:35098800-35104000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr11:35098800-35105400	Weak transcription	Small Intestine	intestine
10	chr11:35099400-35103800	Weak transcription	K562	blood
11	chr11:35099400-35104400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:35099600-35103800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr11:35099600-35104000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr11:35099800-35104000	Weak transcription	Stomach Mucosa	stomach
15	chr11:35099800-35104200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:35100000-35103800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:35100000-35103800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr11:35100000-35103800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:35100000-35103800	Weak transcription	A549	lung
20	chr11:35100000-35103800	Weak transcription	HSMM	muscle
21	chr11:35100000-35103800	Weak transcription	NH-A	brain
22	chr11:35100200-35103600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:35100200-35103800	Enhancers	Primary T cells from cord blood	blood
24	chr11:35100200-35103800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:35100200-35103800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:35100200-35103800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:35100200-35103800	Weak transcription	Esophagus	oesophagus
28	chr11:35100200-35103800	Enhancers	GM12878-XiMat	blood
29	chr11:35100200-35104000	Enhancers	Primary B cells from cord blood	blood
30	chr11:35100400-35103600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:35100400-35103800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr11:35100400-35103800	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr11:35100800-35103800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:35100800-35103800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr11:35101000-35103800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:35101000-35103800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:35101200-35103800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr11:35101400-35103800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr11:35101400-35103800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr11:35101400-35103800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:35101400-35103800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr11:35101400-35103800	Weak transcription	Lung	lung
43	chr11:35102200-35103800	Weak transcription	Dnd41	blood
44	chr11:35102400-35104000	Weak transcription	Thymus	Thymus
45	chr11:35102600-35103600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:35102600-35103800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr11:35103000-35103800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr11:35103000-35104000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:35103200-35103800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:35103200-35103800	Enhancers	Muscle Satellite Cultured Cells	--

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