Variant report

Variant	rs2957268
Chromosome Location	chr11:65245816-65245817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64937399..64939076-chr11:65244914..65247158,2	K562	blood:
2	chr11:65244002..65246872-chr11:65552938..65554614,2	MCF-7	breast:
3	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
4	chr11:65245155..65247560-chr16:24796824..24799252,2	MCF-7	breast:
5	chr11:65245175..65245980-chr20:30192767..30193662,2	Hela-S3	cervix:
6	chr11:65242930..65245954-chr11:65312458..65315573,3	K562	blood:
7	chr11:65243833..65246193-chr6:30583612..30585555,2	MCF-7	breast:
8	chr11:65148785..65152547-chr11:65241836..65246912,8	K562	blood:
9	chr11:65243459..65246387-chr11:65628036..65629552,2	K562	blood:
10	chr11:65244794..65246444-chr17:57922077..57924956,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162241	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000172818	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000172732	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10896001	0.81[AMR][1000 genomes]
rs11227204	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1616810	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1621277	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1626021	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1784100	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1784101	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1784858	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1784859	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1784860	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2105608	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2508711	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2508712	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2846861	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957269	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015965	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3015966	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3016343	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3132742	0.80[AMR][1000 genomes]
rs3132743	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3132767	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs587080	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs587390	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588298	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs591291	0.84[AMR][1000 genomes]
rs602838	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs604676	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605035	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs660588	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs661403	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs682845	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7114809	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7934628	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers 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 miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
15	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
16	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	946 gene(s)	inside rSNPs	diseases
17	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
18	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases
19	nsv541075	chr11:65210592-65331136	Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	620 gene(s)	inside rSNPs	diseases
20	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
21	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2957268	NEAT1	cis	Esophagus Mucosa	GTEx
rs2957268	NEAT1	cis	Muscle Skeletal	GTEx
rs2957268	NEAT1	cis	Nerve Tibial	GTEx
rs2957268	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs2957268	NEAT1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65243800-65246400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:65243800-65246400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:65244200-65246000	Active TSS	Fetal Kidney	kidney
4	chr11:65244200-65246200	Active TSS	Left Ventricle	heart
5	chr11:65244200-65246600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr11:65244200-65246800	Active TSS	Ovary	ovary
7	chr11:65244400-65246000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr11:65244400-65246000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:65244400-65246000	Active TSS	Brain Angular Gyrus	brain
10	chr11:65244400-65246000	Active TSS	Colon Smooth Muscle	Colon
11	chr11:65244400-65246400	Active TSS	Right Ventricle	heart
12	chr11:65244600-65246000	Active TSS	Brain Cingulate Gyrus	brain
13	chr11:65244600-65246000	Active TSS	Fetal Brain Female	brain
14	chr11:65244600-65246000	Active TSS	Rectal Smooth Muscle	rectum
15	chr11:65244600-65246000	Active TSS	GM12878-XiMat	blood
16	chr11:65244800-65246000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:65245000-65247200	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr11:65245200-65246200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr11:65245200-65246200	Flanking Active TSS	Dnd41	blood
20	chr11:65245200-65246200	Flanking Active TSS	K562	blood
21	chr11:65245200-65246800	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr11:65245200-65246800	Flanking Active TSS	Fetal Intestine Large	intestine
23	chr11:65245200-65247000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:65245200-65247000	Flanking Active TSS	Fetal Lung	lung
25	chr11:65245200-65247400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:65245200-65247600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:65245200-65247600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:65245200-65247600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:65245200-65247600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr11:65245200-65247800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:65245200-65247800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr11:65245200-65247800	Flanking Active TSS	Osteobl	bone
33	chr11:65245200-65248000	Flanking Active TSS	Hela-S3	cervix
34	chr11:65245400-65246000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr11:65245400-65246000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr11:65245400-65246200	Active TSS	Right Atrium	heart
37	chr11:65245400-65246400	Weak transcription	Aorta	Aorta
38	chr11:65245400-65246600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr11:65245400-65247000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr11:65245400-65247600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:65245400-65247800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:65245400-65248400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:65245400-65254600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr11:65245600-65246000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr11:65245600-65246000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr11:65245600-65246000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:65245600-65246000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr11:65245600-65246000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr11:65245600-65246000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:65245600-65246000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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