Variant report

Variant	rs11723996
Chromosome Location	chr4:119198888-119198889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:119197988-119206014	GM12878	blood:	n/a	n/a
2	RELA	chr4:119198729-119200786	GM18505	blood:	n/a	n/a
3	MXI1	chr4:119198411-119204666	SK-N-SH	brain:	n/a	n/a
4	MYC	chr4:119198887-119199270	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr4:119198856-119198921	MCF-7	breast:	n/a	n/a
6	POLR2A	chr4:119198623-119205724	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr4:119198552-119205767	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr4:119198541-119204580	GM18505	blood:	n/a	n/a
9	CEBPB	chr4:119198807-119200677	GM12878	blood:	n/a	n/a
10	TBP	chr4:119198813-119201130	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:119198265..119200504-chr4:119654029..119656125,2	K562	blood:
2	chr4:119198319..119200411-chr6:26198105..26199834,2	MCF-7	breast:
3	chr4:119150653..119153442-chr4:119197486..119199123,2	K562	blood:
4	chr4:119198442..119201160-chr4:120987880..120989467,2	MCF-7	breast:
5	chr4:119198677..119205956-chr4:119272273..119279963,18	MCF-7	breast:

No data

Variant related genes	Relation type
SNHG8	TF binding region
ENSG00000197409	Chromatin interaction
ENSG00000150961	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000164109	Chromatin interaction
ENSG00000250938	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000164099	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10001926	0.81[ASN][1000 genomes]
rs10002634	0.93[ASN][1000 genomes]
rs10008013	0.93[ASN][1000 genomes]
rs10014055	0.93[ASN][1000 genomes]
rs10014957	0.93[ASN][1000 genomes]
rs10016206	0.93[ASN][1000 genomes]
rs10016301	0.90[ASN][1000 genomes]
rs10018844	0.93[ASN][1000 genomes]
rs10024837	0.93[ASN][1000 genomes]
rs10025690	0.93[ASN][1000 genomes]
rs10033927	0.93[ASN][1000 genomes]
rs10213280	0.93[ASN][1000 genomes]
rs1028091	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1045817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11723877	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11726746	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11726838	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11727684	0.93[ASN][1000 genomes]
rs11727817	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11728941	0.93[ASN][1000 genomes]
rs11730327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11730687	0.93[ASN][1000 genomes]
rs11731179	0.86[ASN][1000 genomes]
rs11734145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11930782	0.93[ASN][1000 genomes]
rs11933280	0.93[ASN][1000 genomes]
rs11934183	0.93[ASN][1000 genomes]
rs11944227	0.93[ASN][1000 genomes]
rs11945329	0.93[ASN][1000 genomes]
rs11945537	0.93[ASN][1000 genomes]
rs11945882	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11947244	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11947630	0.93[ASN][1000 genomes]
rs13114867	0.90[ASN][1000 genomes]
rs13129847	0.90[ASN][1000 genomes]
rs13435006	0.93[ASN][1000 genomes]
rs1403845	0.93[ASN][1000 genomes]
rs1403846	0.93[ASN][1000 genomes]
rs1523744	0.93[ASN][1000 genomes]
rs1523745	0.93[ASN][1000 genomes]
rs1523746	0.93[ASN][1000 genomes]
rs1589718	0.90[ASN][1000 genomes]
rs17515832	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17516430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17516450	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs17516575	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs17594054	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17594243	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1996725	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2030633	0.93[ASN][1000 genomes]
rs2030634	0.93[ASN][1000 genomes]
rs2204269	0.93[ASN][1000 genomes]
rs2271577	0.93[ASN][1000 genomes]
rs2271578	0.93[ASN][1000 genomes]
rs2272160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28396217	0.93[ASN][1000 genomes]
rs28508556	0.93[ASN][1000 genomes]
rs28661939	1.00[CEU][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805195	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3817274	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4546315	0.93[ASN][1000 genomes]
rs56007507	0.93[ASN][1000 genomes]
rs56258393	0.93[ASN][1000 genomes]
rs56305917	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56339949	0.93[ASN][1000 genomes]
rs56390335	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57605165	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58798110	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60858456	0.86[ASN][1000 genomes]
rs61342457	0.93[ASN][1000 genomes]
rs61443542	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62326151	0.93[ASN][1000 genomes]
rs6534088	0.86[ASN][1000 genomes]
rs6822408	0.86[ASN][1000 genomes]
rs6822996	0.93[ASN][1000 genomes]
rs6842372	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6842689	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6853304	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6853879	0.90[ASN][1000 genomes]
rs6855052	0.93[ASN][1000 genomes]
rs6855536	0.84[ASN][1000 genomes]
rs6856076	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71608347	0.90[ASN][1000 genomes]
rs71608349	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72907147	0.86[ASN][1000 genomes]
rs72907175	0.86[ASN][1000 genomes]
rs72909175	0.93[ASN][1000 genomes]
rs72909186	0.93[ASN][1000 genomes]
rs72917104	0.93[ASN][1000 genomes]
rs72917146	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72917175	0.93[ASN][1000 genomes]
rs72917179	0.93[ASN][1000 genomes]
rs7661522	0.90[ASN][1000 genomes]
rs7685455	0.93[ASN][1000 genomes]
rs9992827	0.90[ASN][1000 genomes]
rs9996753	0.93[ASN][1000 genomes]
rs9996762	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1009076	chr4:118949490-119269424	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1001236	chr4:118949490-119271243	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv34038	chr4:119035124-119455391	Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1001138	chr4:119095147-119461837	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv537230	chr4:119095147-119461837	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1002771	chr4:119125361-119571237	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1003731	chr4:119138262-119506032	Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv1794655	chr4:119170156-119212103	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11723996	SNHG8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119187200-119199000	Weak transcription	Colonic Mucosa	Colon
2	chr4:119187200-119199400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:119195000-119199000	Weak transcription	Osteobl	bone
4	chr4:119195400-119199000	Weak transcription	Primary T cells from cord blood	blood
5	chr4:119196800-119199000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr4:119197000-119199000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr4:119197200-119199000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr4:119197600-119199000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:119197600-119199200	Weak transcription	Pancreas	Pancrea
10	chr4:119197600-119199400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:119197800-119200800	Active TSS	Duodenum Mucosa	Duodenum
12	chr4:119198000-119199000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:119198000-119199000	Enhancers	A549	lung
14	chr4:119198200-119199000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:119198200-119200200	Active TSS	GM12878-XiMat	blood
16	chr4:119198400-119199000	Enhancers	Primary B cells from peripheral blood	blood
17	chr4:119198400-119199000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr4:119198400-119199000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr4:119198400-119199000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:119198400-119199000	Enhancers	Dnd41	blood
21	chr4:119198400-119199200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr4:119198400-119199200	Enhancers	Fetal Thymus	thymus
23	chr4:119198400-119199400	Flanking Active TSS	Fetal Intestine Large	intestine
24	chr4:119198600-119199000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:119198600-119199000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:119198600-119199000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr4:119198600-119199000	Enhancers	Stomach Mucosa	stomach
28	chr4:119198600-119199200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:119198600-119199400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:119198600-119201000	Active TSS	Liver	Liver
31	chr4:119198800-119199000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:119198800-119199000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:119198800-119199000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr4:119198800-119199000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:119198800-119199000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:119198800-119199000	Enhancers	Brain Cingulate Gyrus	brain
37	chr4:119198800-119199000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr4:119198800-119199000	Flanking Active TSS	HepG2	liver
39	chr4:119198800-119199200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:119198800-119199200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr4:119198800-119199200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr4:119198800-119199400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr4:119198800-119199400	Flanking Active TSS	Fetal Intestine Small	intestine
44	chr4:119198800-119199400	Flanking Active TSS	NHEK	skin
45	chr4:119198800-119199600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:119198800-119200200	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr4:119198800-119200200	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr4:119198800-119200400	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr4:119198800-119200400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr4:119198800-119200400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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