Variant report

Variant	rs34913869
Chromosome Location	chr4:119199241-119199242
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	MYBL2	chr4:119199192-119200727	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:119198979-119204800	PBDE	blood:	n/a	n/a
4	YY1	chr4:119199237-119200425	GM12878	blood:	n/a	chr4:119199745-119199756 chr4:119200221-119200233
5	TAF1	chr4:119199239-119200450	K562	blood:	n/a	n/a
6	NRF1	chr4:119199086-119200330	SK-N-SH	brain:	n/a	chr4:119199690-119199699 chr4:119199690-119199701 chr4:119199689-119199700 chr4:119199687-119199701
7	POLR2A	chr4:119199070-119205417	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr4:119199069-119202589	GM12878	blood:	n/a	n/a
9	RCOR1	chr4:119199075-119200229	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:119199241-119200546	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr4:119199204-119204663	HCT-116	colon:	n/a	n/a
12	RELA	chr4:119199174-119200982	GM19193	blood:	n/a	n/a
13	TBL1XR1	chr4:119199032-119200403	GM12878	blood:	n/a	n/a
14	MXI1	chr4:119199196-119200976	IMR90	lung:	n/a	n/a
15	POLR2A	chr4:119198968-119204881	K562	blood:	n/a	n/a
16	MTA3	chr4:119199151-119199709	GM12878	blood:	n/a	n/a
17	EP300	chr4:119199167-119200341	GM12878	blood:	n/a	chr4:119199594-119199603 chr4:119199817-119199830
18	POLR2A	chr4:119199147-119204752	K562	blood:	n/a	n/a
19	POLR2A	chr4:119199152-119204709	K562	blood:	n/a	n/a
20	POLR2A	chr4:119199115-119204889	GM12892	blood:	n/a	n/a
21	IRF1	chr4:119198889-119203207	K562	blood:	n/a	chr4:119199812-119199826 chr4:119198955-119198966 chr4:119198952-119198965 chr4:119200643-119200660 chr4:119199835-119199849
22	RELA	chr4:119198729-119200786	GM18505	blood:	n/a	n/a
23	ELF1	chr4:119199238-119200364	GM12878	blood:	n/a	chr4:119199338-119199351
24	MAX	chr4:119199134-119200652	HCT-116	colon:	n/a	chr4:119199734-119199749 chr4:119199711-119199722
25	MYC	chr4:119199183-119204435	K562	blood:	n/a	chr4:119199734-119199749 chr4:119199711-119199722
26	MXI1	chr4:119198411-119204666	SK-N-SH	brain:	n/a	n/a
27	MYC	chr4:119198887-119199270	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr4:119199010-119204847	GM19099	blood:	n/a	n/a
29	ELF1	chr4:119199240-119199437	K562	blood:	n/a	chr4:119199338-119199351
30	POLR2A	chr4:119199240-119204755	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr4:119199230-119200813	GM12891	blood:	n/a	n/a
32	POLR2A	chr4:119198623-119205724	MCF10A-Er-Src	breast:	n/a	n/a
33	CUX1	chr4:119199136-119200588	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:119198552-119205767	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr4:119198541-119204580	GM18505	blood:	n/a	n/a
36	POLR2A	chr4:119199134-119204712	K562	blood:	n/a	n/a
37	PML	chr4:119199147-119204261	GM12878	blood:	n/a	n/a
38	POLR2A	chr4:119199233-119204730	U87	brain:	n/a	n/a
39	POLR2A	chr4:119199034-119204440	GM12892	blood:	n/a	n/a
40	POLR2A	chr4:119199135-119204787	Raji	blood:	n/a	n/a
41	MYC	chr4:119199160-119201020	K562	blood:	n/a	chr4:119199734-119199749 chr4:119199711-119199722
42	MXI1	chr4:119199121-119200697	GM12878	blood:	n/a	n/a
43	RUNX3	chr4:119199156-119200474	GM12878	blood:	n/a	n/a
44	YY1	chr4:119199200-119199463	SK-N-SH_RA	brain:	n/a	n/a
45	POLR2A	chr4:119199236-119204354	GM19193	blood:	n/a	n/a
46	WRNIP1	chr4:119199223-119200903	GM12878	blood:	n/a	n/a
47	CEBPB	chr4:119199127-119200230	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr4:119199097-119205823	GM12891	blood:	n/a	n/a
49	CHD1	chr4:119199106-119201331	GM12878	blood:	n/a	chr4:119199814-119199824
50	CUX1	chr4:119199069-119199354	K562	blood:	n/a	n/a

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	chr11:65195812..65196754-chr4:119199186..119199806,2	Hela-S3	cervix:
4	chr4:119198442..119201160-chr4:120987880..120989467,2	MCF-7	breast:
5	chr14:103986983..103987911-chr4:119199083..119199796,2	Hela-S3	cervix:
6	chr17:73775421..73776209-chr4:119199186..119199806,2	Hela-S3	cervix:
7	chr4:119198677..119205956-chr4:119272273..119279963,18	MCF-7	breast:

Variant related genes	Relation type
SNHG8	TF binding region
ENSG00000196866	Chromatin interaction
ENSG00000150961	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000164099	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000164109	Chromatin interaction
ENSG00000166165	Chromatin interaction
ENSG00000250938	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10030445	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098432	0.81[ASN][1000 genomes]
rs11947394	0.89[ASN][1000 genomes]
rs13132331	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13145025	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1573955	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17642201	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1949760	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2138009	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389567	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28620219	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892800	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34399419	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3805189	0.80[ASN][1000 genomes]
rs3828500	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4327555	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4833570	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833572	0.81[AFR][1000 genomes]
rs4834670	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4834672	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4834675	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834677	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834678	0.82[AFR][1000 genomes]
rs59998459	0.82[EUR][1000 genomes]
rs6825871	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7674426	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690554	0.81[AFR][1000 genomes]
rs9685810	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972813	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9884481	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34913869	SNHG8	cis	Skin Sun Exposed Lower leg	GTEx
rs34913869	SNHG8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119187200-119199400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:119197600-119199400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:119197800-119200800	Active TSS	Duodenum Mucosa	Duodenum
4	chr4:119198200-119200200	Active TSS	GM12878-XiMat	blood
5	chr4:119198400-119199400	Flanking Active TSS	Fetal Intestine Large	intestine
6	chr4:119198600-119199400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:119198600-119201000	Active TSS	Liver	Liver
8	chr4:119198800-119199400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr4:119198800-119199400	Flanking Active TSS	Fetal Intestine Small	intestine
10	chr4:119198800-119199400	Flanking Active TSS	NHEK	skin
11	chr4:119198800-119199600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:119198800-119200200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr4:119198800-119200200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr4:119198800-119200400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr4:119198800-119200400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr4:119198800-119200400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:119198800-119200400	Active TSS	K562	blood
18	chr4:119198800-119200600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:119198800-119200600	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr4:119198800-119200600	Active TSS	NH-A	brain
21	chr4:119199000-119199400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:119199000-119199400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr4:119199000-119199400	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr4:119199000-119199400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:119199000-119199400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr4:119199000-119199400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr4:119199000-119199400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:119199000-119199400	Active TSS	Muscle Satellite Cultured Cells	--
29	chr4:119199000-119199400	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr4:119199000-119199400	Enhancers	Fetal Heart	heart
31	chr4:119199000-119199400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr4:119199000-119199400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr4:119199000-119199600	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr4:119199000-119199600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr4:119199000-119199600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:119199000-119199600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:119199000-119199600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:119199000-119199800	Flanking Active TSS	Dnd41	blood
39	chr4:119199000-119200000	Active TSS	HepG2	liver
40	chr4:119199000-119200200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr4:119199000-119200200	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr4:119199000-119200200	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr4:119199000-119200200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
44	chr4:119199000-119200400	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr4:119199000-119200400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:119199000-119200400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:119199000-119200400	Active TSS	Fetal Brain Male	brain
48	chr4:119199000-119200400	Active TSS	HMEC	breast
49	chr4:119199000-119200400	Active TSS	Osteobl	bone
50	chr4:119199000-119200600	Active TSS	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links