Variant report

Variant	rs929934
Chromosome Location	chr11:57411252-57411253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57410796-57421100	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:57404829-57418710	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr11:57410916-57411627	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr11:57410821-57420904	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:57404802-57417187	SK-N-MC	brain:	n/a	n/a
6	CTCF	chr11:57411180-57411330	AG04450	lung:	n/a	n/a
7	POLR2A	chr11:57410853-57411488	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr11:57410100-57417938	PBDE	blood:	n/a	n/a
9	POLR2A	chr11:57411157-57411607	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr11:57411114-57411673	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr11:57409804-57420281	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr11:57411074-57411825	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr11:57410944-57411528	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:57411096-57411652	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57334278..57336865-chr11:57411196..57413730,2	K562	blood:
2	chr11:57334539..57338384-chr11:57406664..57411574,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000254602	TF binding region
ENSG00000156587	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10792110	0.88[JPT][hapmap]
rs10896644	1.00[JPT][hapmap]
rs10896649	0.88[JPT][hapmap]
rs11229109	0.88[JPT][hapmap]
rs11570176	1.00[JPT][hapmap]
rs11570181	1.00[JPT][hapmap]
rs1613592	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1631684	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1647394	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1647403	0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17455422	1.00[JPT][hapmap]
rs1783826	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1783827	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1783828	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1783829	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1783978	1.00[JPT][hapmap]
rs1783979	1.00[JPT][hapmap]
rs1783980	0.88[JPT][hapmap]
rs1783981	0.88[JPT][hapmap]
rs1783983	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1783984	0.82[AMR][1000 genomes]
rs1783985	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1785498	0.86[JPT][hapmap]
rs1798172	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1798173	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1798177	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2156638	0.88[JPT][hapmap]
rs2956981	1.00[JPT][hapmap]
rs3017889	1.00[JPT][hapmap]
rs36036499	1.00[JPT][hapmap]
rs4611222	0.88[JPT][hapmap]
rs627145	1.00[JPT][hapmap]
rs653889	1.00[JPT][hapmap]
rs665058	1.00[JPT][hapmap]
rs7117020	1.00[JPT][hapmap]
rs7120868	1.00[JPT][hapmap]
rs7947357	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' 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	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	esv992553	chr11:57408294-57419351	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs929934	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs929934	YPEL4	cis	lung	GTEx
rs929934	TIMM10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57403000-57412200	Weak transcription	Hela-S3	cervix
2	chr11:57407200-57412200	Weak transcription	Ovary	ovary
3	chr11:57407400-57412600	Weak transcription	GM12878-XiMat	blood
4	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr11:57407600-57412200	Weak transcription	Spleen	Spleen
7	chr11:57407600-57413000	Weak transcription	Right Ventricle	heart
8	chr11:57407600-57413200	Weak transcription	Esophagus	oesophagus
9	chr11:57407800-57412200	Weak transcription	Pancreas	Pancrea
10	chr11:57408000-57412000	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:57408000-57412200	Weak transcription	Lung	lung
12	chr11:57408200-57411400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:57408200-57411400	Genic enhancers	Fetal Muscle Leg	muscle
14	chr11:57408200-57412000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:57408200-57412000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:57408400-57412200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:57408800-57411600	Genic enhancers	H1 Cell Line	embryonic stem cell
18	chr11:57408800-57411800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:57408800-57412000	Weak transcription	Left Ventricle	heart
20	chr11:57408800-57412000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr11:57408800-57412000	Weak transcription	Right Atrium	heart
22	chr11:57408800-57412200	Weak transcription	Adipose Nuclei	Adipose
23	chr11:57408800-57412200	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:57408800-57412200	Weak transcription	Thymus	Thymus
25	chr11:57408800-57412600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:57408800-57412600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:57408800-57413400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr11:57409000-57411400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:57409000-57411600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
30	chr11:57409000-57411600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr11:57409000-57412000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:57409000-57412000	Weak transcription	Brain Angular Gyrus	brain
33	chr11:57409000-57412000	Weak transcription	Brain Anterior Caudate	brain
34	chr11:57409000-57412000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:57409000-57412000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr11:57409000-57412200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr11:57409000-57412200	Weak transcription	Brain Substantia Nigra	brain
38	chr11:57409000-57412200	Weak transcription	Fetal Intestine Small	intestine
39	chr11:57409000-57412200	Weak transcription	Fetal Kidney	kidney
40	chr11:57409000-57412200	Weak transcription	A549	lung
41	chr11:57409000-57412200	Weak transcription	HSMMtube	muscle
42	chr11:57409000-57413200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:57409000-57414400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:57409000-57416200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr11:57409200-57411400	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr11:57409200-57412000	Weak transcription	Fetal Brain Male	brain
47	chr11:57409200-57412200	Weak transcription	Liver	Liver
48	chr11:57409200-57412200	Weak transcription	HepG2	liver
49	chr11:57409200-57412200	Weak transcription	Osteobl	bone
50	chr11:57409200-57413600	Weak transcription	Primary T cells from cord blood	blood

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