Variant report

Variant	rs2904975
Chromosome Location	chr11:65173754-65173755
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	chr11:65171068..65175502-chr11:65265167..65268123,5	K562	blood:

Variant related genes	Relation type
ENSG00000270117	Chromatin interaction
ENSG00000251562	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs512715	0.80[AMR][1000 genomes]
rs595366	0.81[AMR][1000 genomes]
rs674485	0.81[AMR][1000 genomes]
rs694243	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2904975	NEAT1	cis	Muscle Skeletal	GTEx
rs2904975	NEAT1	cis	Nerve Tibial	GTEx
rs2904975	NEAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs2904975	NEAT1	cis	Esophagus Mucosa	GTEx
rs2904975	NEAT1	cis	Thyroid	GTEx
rs2904975	NEAT1	cis	Adipose Subcutaneous	GTEx
rs2904975	NEAT1	cis	Esophagus Muscularis	GTEx
rs2904975	NEAT1	cis	Artery Tibial	GTEx
rs2904975	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs2904975	NEAT1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65157200-65182800	Weak transcription	Psoas Muscle	Psoas
2	chr11:65158600-65183200	Weak transcription	Fetal Brain Male	brain
3	chr11:65158600-65183400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:65158800-65183000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:65158800-65183400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:65159000-65183800	Weak transcription	Fetal Kidney	kidney
7	chr11:65159200-65182000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:65159400-65180800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:65159400-65181600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:65159400-65181800	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr11:65159400-65182200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:65159600-65179400	Weak transcription	Right Atrium	heart
13	chr11:65159600-65181800	Strong transcription	Fetal Stomach	stomach
14	chr11:65159600-65183400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:65159800-65174200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:65159800-65181800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:65159800-65183000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:65160000-65176000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:65160200-65179800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:65160800-65181800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:65161200-65181400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:65162800-65183400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:65167400-65177800	Strong transcription	Osteobl	bone
24	chr11:65168200-65177200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:65168600-65176000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr11:65168600-65178800	Weak transcription	Small Intestine	intestine
27	chr11:65168800-65177000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:65169800-65175800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr11:65170200-65174200	Strong transcription	Pancreas	Pancrea
30	chr11:65170200-65175800	Weak transcription	NH-A	brain
31	chr11:65170400-65183600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:65170600-65176000	Weak transcription	HepG2	liver
33	chr11:65170800-65179600	Strong transcription	Brain Anterior Caudate	brain
34	chr11:65171000-65174000	Strong transcription	Brain Germinal Matrix	brain
35	chr11:65171200-65175000	Strong transcription	Ovary	ovary
36	chr11:65171200-65177200	Genic enhancers	Primary B cells from peripheral blood	blood
37	chr11:65171200-65179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:65171200-65184200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:65171400-65183200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr11:65171600-65174200	Strong transcription	Esophagus	oesophagus
41	chr11:65171800-65174000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr11:65171800-65174400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr11:65171800-65178600	Strong transcription	Fetal Intestine Large	intestine
44	chr11:65171800-65179200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:65171800-65180400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr11:65171800-65180400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr11:65171800-65181800	Strong transcription	Lung	lung
48	chr11:65172000-65176000	Weak transcription	Stomach Mucosa	stomach
49	chr11:65172000-65179200	Strong transcription	Left Ventricle	heart
50	chr11:65172000-65180400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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