Variant report

Variant	rs694243
Chromosome Location	chr11:65172197-65172198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65171611..65173727-chr11:65270547..65272870,2	K562	blood:
2	chr11:65171068..65175502-chr11:65265167..65268123,5	K562	blood:
3	chr11:65171200..65173493-chr11:65236572..65239477,2	K562	blood:
4	chr11:65156578..65159572-chr11:65170803..65173181,2	K562	blood:
5	chr11:65171845..65173402-chr11:65273190..65275037,2	K562	blood:

Variant related genes	Relation type
ENSG00000251562	Chromatin interaction
ENSG00000270117	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs1621277	0.83[MEX][hapmap]
rs1626021	0.83[MEX][hapmap]
rs1784859	0.83[MEX][hapmap]
rs2846861	0.83[MEX][hapmap]
rs2904975	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs512715	0.83[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs588298	0.83[MEX][hapmap]
rs595366	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs613316	0.80[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs674485	0.88[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs694243	NEAT1	cis	Adipose Subcutaneous	GTEx
rs694243	CDK2AP2	cis	cerebellum	SCAN
rs694243	PYGM	cis	cerebellum	SCAN
rs694243	NEAT1	cis	Artery Tibial	GTEx
rs694243	NEAT1	cis	Muscle Skeletal	GTEx
rs694243	STX5	cis	parietal	SCAN
rs694243	NEAT1	cis	Nerve Tibial	GTEx
rs694243	NEAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs694243	NEAT1	cis	Esophagus Mucosa	GTEx
rs694243	MALAT1	cis	parietal	SCAN
rs694243	VWCE	cis	parietal	SCAN
rs694243	SCGB2A2	cis	parietal	SCAN
rs694243	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs694243	NEAT1	cis	lung	GTEx
rs694243	NEAT1	cis	Thyroid	GTEx
rs694243	NEAT1	cis	Esophagus Muscularis	GTEx
rs694243	NEAT1	cis	brain	BrainEAC
rs694243	TPCN2	cis	parietal	SCAN

Chromatin state (count:124 , 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	chr11:65158800-65172200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:65158800-65183000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:65158800-65183400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:65159000-65173400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr11:65159000-65183800	Weak transcription	Fetal Kidney	kidney
9	chr11:65159200-65182000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr11:65159400-65180800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:65159400-65181600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:65159400-65181800	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr11:65159400-65182200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:65159600-65172600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:65159600-65173400	Strong transcription	Brain Cingulate Gyrus	brain
16	chr11:65159600-65179400	Weak transcription	Right Atrium	heart
17	chr11:65159600-65181800	Strong transcription	Fetal Stomach	stomach
18	chr11:65159600-65183400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:65159800-65174200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:65159800-65181800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:65159800-65183000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:65160000-65176000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:65160200-65179800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:65160600-65172600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:65160800-65181800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr11:65161200-65172400	Strong transcription	Right Ventricle	heart
27	chr11:65161200-65181400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:65162800-65183400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:65163400-65173400	Strong transcription	Rectal Smooth Muscle	rectum
30	chr11:65166400-65172400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:65167400-65177800	Strong transcription	Osteobl	bone
32	chr11:65167600-65172400	Genic enhancers	Fetal Intestine Small	intestine
33	chr11:65167600-65172800	Strong transcription	HUVEC	blood vessel
34	chr11:65168200-65177200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr11:65168600-65172200	Weak transcription	Aorta	Aorta
36	chr11:65168600-65172400	Weak transcription	HSMMtube	muscle
37	chr11:65168600-65176000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr11:65168600-65178800	Weak transcription	Small Intestine	intestine
39	chr11:65168800-65172200	Weak transcription	HMEC	breast
40	chr11:65168800-65177000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr11:65169000-65173200	Enhancers	Primary hematopoietic stem cells	blood
42	chr11:65169800-65172800	Strong transcription	Hela-S3	cervix
43	chr11:65169800-65173400	Strong transcription	HSMM	muscle
44	chr11:65169800-65175800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:65170200-65173400	Enhancers	Primary B cells from cord blood	blood
46	chr11:65170200-65174200	Strong transcription	Pancreas	Pancrea
47	chr11:65170200-65175800	Weak transcription	NH-A	brain
48	chr11:65170400-65172200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr11:65170400-65172600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr11:65170400-65173400	Strong transcription	Dnd41	blood

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