Variant report

Variant	rs512715
Chromosome Location	chr11:65191208-65191209
allele	C/G
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:87)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:87 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr11:65189745..65191975-chr6:26031207..26033394,2	K562	blood:
2	chr11:65082107..65083673-chr11:65189217..65191365,2	MCF-7	breast:
3	chr11:65053101..65054980-chr11:65191056..65193756,3	K562	blood:
4	chr11:65189010..65195293-chr11:65321323..65327708,15	K562	blood:
5	chr11:65190371..65192936-chr6:31618230..31620421,2	MCF-7	breast:
6	chr11:65190400..65191290-chr8:133787467..133788135,2	Hela-S3	cervix:
7	chr11:65190238..65193171-chr13:92003562..92006013,2	K562	blood:
8	chr10:27530518..27532485-chr11:65188635..65191492,2	MCF-7	breast:
9	chr11:62607615..62610579-chr11:65189094..65191693,2	MCF-7	breast:
10	chr11:65187744..65191441-chr11:65307194..65309813,3	MCF-7	breast:
11	chr11:65190846..65191515-chr4:102268160..102269031,2	HCT-116	colon:
12	chr11:65057209..65061295-chr11:65190411..65193385,3	K562	blood:
13	chr11:64999920..65001432-chr11:65190879..65192443,2	K562	blood:
14	chr11:64018454..64020454-chr11:65189395..65191669,2	MCF-7	breast:
15	chr11:65188258..65192947-chr11:65311570..65315780,5	MCF-7	breast:
16	chr11:65190681..65191412-chr3:138312686..138313279,2	HCT-116	colon:
17	chr11:65190798..65191686-chrX:44732399..44733466,3	Hela-S3	cervix:
18	chr1:8085697..8086453-chr11:65190418..65191405,2	Hela-S3	cervix:
19	chr11:65190400..65192835-chr7:104653027..104654688,2	K562	blood:
20	chr11:65190161..65193929-chr17:59476956..59480011,3	MCF-7	breast:
21	chr11:65028103..65030991-chr11:65188788..65191974,4	K562	blood:
22	chr11:65190656..65191526-chr17:40724113..40724630,2	Hela-S3	cervix:
23	chr11:65190482..65192896-chr21:47740490..47743201,2	K562	blood:
24	chr11:65190432..65191363-chr2:24307494..24308137,2	Hela-S3	cervix:
25	chr11:65191125..65191738-chr16:4320862..4321807,2	Hela-S3	cervix:
26	chr11:10829969..10830483-chr11:65191139..65191689,2	Hela-S3	cervix:
27	chr11:65191038..65191994-chr3:160282483..160283152,2	Hela-S3	cervix:
28	chr11:65186294..65191468-chr11:65379126..65384544,8	MCF-7	breast:
29	chr11:65190162..65194738-chr11:65316952..65321274,6	K562	blood:
30	chr11:65190823..65192325-chr11:65659028..65661799,2	K562	blood:
31	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
32	chr11:65184392..65191686-chr11:65339528..65345365,10	K562	blood:
33	chr11:65190713..65191489-chr17:7475150..7475795,2	Hela-S3	cervix:
34	chr11:65190192..65192335-chr13:91999791..92002488,2	K562	blood:
35	chr11:65089150..65091155-chr11:65191102..65193583,2	K562	blood:
36	chr11:65191050..65192675-chr17:7481475..7484136,2	K562	blood:
37	chr11:65190366..65193002-chr19:12897399..12898965,2	MCF-7	breast:
38	chr11:65190837..65192607-chr11:65358466..65361210,2	MCF-7	breast:
39	chr11:65082099..65083915-chr11:65190735..65192502,3	K562	blood:
40	chr11:65189137..65192069-chr11:65349973..65352376,3	K562	blood:
41	chr11:65190582..65191212-chr12:31812117..31812764,2	Hela-S3	cervix:
42	chr11:65188021..65191759-chr11:65338955..65343877,5	MCF-7	breast:
43	chr11:65190679..65191429-chr3:129034879..129035643,2	HCT-116	colon:
44	chr11:64973188..64975760-chr11:65189553..65191524,2	K562	blood:
45	chr11:65190676..65193675-chr15:44089126..44092016,2	MCF-7	breast:
46	chr1:226250340..226251106-chr11:65190475..65191376,2	Hela-S3	cervix:
47	chr11:65190724..65191290-chr17:57920469..57921363,2	Hela-S3	cervix:
48	chr11:65190743..65191615-chr17:75084363..75085087,2	Hela-S3	cervix:
49	chr11:65189570..65191757-chr11:66239067..66241497,2	MCF-7	breast:
50	chr11:65189521..65192173-chr17:56736309..56738189,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP000769.1-2	chr11:65190766-65194537	NONHSAT022114

No data

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000147050	Chromatin interaction
ENSG00000006025	Chromatin interaction
ENSG00000179262	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000129657	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000115129	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000270526	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000138814	Chromatin interaction
ENSG00000140443	Chromatin interaction
ENSG00000149798	Chromatin interaction
ENSG00000114107	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000107438	Chromatin interaction
ENSG00000234912	Chromatin interaction
ENSG00000204444	Chromatin interaction
ENSG00000260233	Chromatin interaction
ENSG00000263800	Chromatin interaction
ENSG00000129226	Chromatin interaction
ENSG00000254531	Chromatin interaction
ENSG00000005483	Chromatin interaction
ENSG00000149782	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000269018	Chromatin interaction
ENSG00000078967	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000184716	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000262412	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000107290	Chromatin interaction
ENSG00000173727	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000177192	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000173338	Chromatin interaction
ENSG00000139160	Chromatin interaction
ENSG00000124181	Chromatin interaction
ENSG00000129292	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000184897	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000107897	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000160298	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000175315	Chromatin interaction
ENSG00000222724	Chromatin interaction
ENSG00000177125	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000239569	Chromatin interaction
ENSG00000175592	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000255992	Chromatin interaction
ENSG00000174516	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000116285	Chromatin interaction
ENSG00000142186	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000176973	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:12)

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	0.80[AMR][1000 genomes]
rs580933	0.81[JPT][hapmap]
rs588298	0.83[MEX][hapmap]
rs595366	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs613316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs673753	0.81[JPT][hapmap]
rs674485	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694243	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]

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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs512715	VWCE	cis	parietal	SCAN
rs512715	NEAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs512715	STX5	cis	parietal	SCAN
rs512715	AK027191	cis	multi-tissue	Pritchard
rs512715	SCGB2A2	cis	parietal	SCAN
rs512715	MALAT1	cis	parietal	SCAN
rs512715	NM_138368	cis	multi-tissue	Pritchard
rs512715	NEAT1	cis	Adipose Subcutaneous	GTEx
rs512715	CDK2AP2	cis	cerebellum	SCAN
rs512715	NEAT1	cis	Artery Tibial	GTEx
rs512715	NEAT1	cis	Esophagus Mucosa	GTEx
rs512715	TPCN2	cis	parietal	SCAN
rs512715	NEAT1	cis	Nerve Tibial	GTEx
rs512715	NEAT1	cis	lung	GTEx
rs512715	NEAT1	cis	Esophagus Muscularis	GTEx
rs512715	NEAT1	cis	Muscle Skeletal	GTEx
rs512715	NEAT1	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65183600-65194200	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr11:65186000-65193800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr11:65186000-65195000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
4	chr11:65186200-65192400	Active TSS	Right Ventricle	heart
5	chr11:65186200-65197400	Active TSS	Psoas Muscle	Psoas
6	chr11:65186800-65191800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr11:65188000-65194200	Active TSS	Liver	Liver
8	chr11:65188400-65191400	Active TSS	Left Ventricle	heart
9	chr11:65188400-65191800	Active TSS	Sigmoid Colon	Sigmoid Colon
10	chr11:65188400-65193600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr11:65188400-65194400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:65188400-65194600	Active TSS	Esophagus	oesophagus
13	chr11:65188600-65191400	Active TSS	Aorta	Aorta
14	chr11:65188600-65191600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:65188600-65193000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:65188600-65194000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr11:65188600-65194000	Active TSS	HSMMtube	muscle
18	chr11:65188800-65194000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:65188800-65194000	Active TSS	Lung	lung
20	chr11:65189000-65193600	Active TSS	Spleen	Spleen
21	chr11:65189000-65193800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr11:65189000-65194600	Active TSS	Pancreas	Pancrea
23	chr11:65189200-65191400	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr11:65189200-65191400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:65189200-65191400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:65189200-65191400	Active TSS	Brain Anterior Caudate	brain
27	chr11:65189200-65191400	Active TSS	Brain Cingulate Gyrus	brain
28	chr11:65189200-65191600	Active TSS	Brain Substantia Nigra	brain
29	chr11:65189200-65191800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:65189200-65191800	Active TSS	HSMM	muscle
31	chr11:65189200-65192800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:65189200-65193000	Bivalent/Poised TSS	HepG2	liver
33	chr11:65189200-65193800	Active TSS	Fetal Heart	heart
34	chr11:65189200-65193800	Active TSS	Fetal Kidney	kidney
35	chr11:65189200-65194800	Active TSS	Small Intestine	intestine
36	chr11:65189400-65191400	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr11:65189400-65191600	Active TSS	GM12878-XiMat	blood
38	chr11:65189400-65191800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr11:65189400-65193000	Active TSS	Gastric	stomach
40	chr11:65189400-65194200	Active TSS	Placenta Amnion	Placenta Amnion
41	chr11:65189400-65194400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:65189400-65195600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:65189400-65195800	Active TSS	Ovary	ovary
44	chr11:65189600-65191400	Active TSS	Duodenum Mucosa	Duodenum
45	chr11:65189600-65191400	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr11:65189600-65191400	Active TSS	Hela-S3	cervix
47	chr11:65189600-65191800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:65189600-65191800	Active TSS	Brain Hippocampus Middle	brain
49	chr11:65189600-65191800	Active TSS	Placenta	Placenta
50	chr11:65189600-65192600	Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links