Variant report

Variant	rs11829917
Chromosome Location	chr12:58164455-58164456
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58164350-58167067	K562	blood:	n/a	n/a
2	PAX5	chr12:58164443-58164655	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:58162820-58164727	A549	lung:	n/a	n/a
4	POLR2A	chr12:58164078-58166934	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:58164424-58166975	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:58163238..58167741-chr12:58238267..58242135,5	MCF-7	breast:
2	chr12:58164080..58166342-chr12:58209150..58210978,2	K562	blood:
3	chr12:57983700..57986584-chr12:58162901..58165594,2	K562	blood:
4	chr12:58163290..58165858-chr12:58229463..58232387,2	K562	blood:
5	chr12:58162243..58164732-chr12:58237977..58240961,2	K562	blood:
6	chr12:57823258..57825830-chr12:58164419..58166506,2	MCF-7	breast:
7	chr12:58004396..58008788-chr12:58163385..58167140,4	MCF-7	breast:
8	chr12:57913372..57915977-chr12:58164344..58168645,6	K562	blood:
9	chr12:58164032..58167803-chr12:58328284..58330655,5	K562	blood:
10	chr12:57912814..57915992-chr12:58164344..58170030,6	K562	blood:

No data

Variant related genes	Relation type
METTL21B	TF binding region
CYP27B1	TF binding region
METTL1	TF binding region
ENSG00000257921	TF binding region
ENSG00000240771	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000257698	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000257953	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000175197	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11172322	0.87[ASW][hapmap];0.91[YRI][hapmap]
rs11172325	0.87[ASW][hapmap];0.91[YRI][hapmap]
rs11172336	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11172339	0.83[AMR][1000 genomes]
rs11172348	0.95[LWK][hapmap];1.00[MEX][hapmap]
rs11555555	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297574	1.00[AMR][1000 genomes]
rs12297635	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297639	0.83[AMR][1000 genomes]
rs12321371	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1389302	0.83[AMR][1000 genomes]
rs3211638	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3472	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3473	0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs36227551	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74094230	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
7	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11829917	MEST	trans	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58160800-58164600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58160800-58164600	Weak transcription	Right Atrium	heart
3	chr12:58160800-58165200	Weak transcription	Brain Substantia Nigra	brain
4	chr12:58161000-58164800	Weak transcription	Right Ventricle	heart
5	chr12:58161000-58165200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:58161000-58165200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:58161000-58165200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:58161200-58164600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:58161200-58164800	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:58161200-58164800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:58161200-58165000	Weak transcription	NH-A	brain
12	chr12:58161200-58165200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:58161400-58164600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:58161400-58164600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:58161400-58164800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:58161400-58164800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:58161400-58164800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:58161400-58164800	Weak transcription	HUVEC	blood vessel
19	chr12:58161400-58165200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:58161400-58165200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:58161400-58165200	Weak transcription	Colonic Mucosa	Colon
22	chr12:58161600-58164600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:58161600-58164600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:58161600-58164800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:58161600-58164800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:58161600-58164800	Weak transcription	NHDF-Ad	bronchial
27	chr12:58161800-58164600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:58161800-58164600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:58161800-58164600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:58161800-58164800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:58161800-58164800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:58161800-58164800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:58161800-58164800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:58161800-58164800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:58161800-58164800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr12:58162000-58164600	Strong transcription	Adipose Nuclei	Adipose
37	chr12:58162000-58164600	Strong transcription	Fetal Intestine Small	intestine
38	chr12:58162000-58164600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr12:58162000-58164600	Strong transcription	Placenta	Placenta
40	chr12:58162000-58164600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr12:58162000-58164800	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr12:58162000-58164800	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr12:58162000-58164800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:58162000-58164800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:58162000-58164800	Strong transcription	Liver	Liver
46	chr12:58162000-58164800	Strong transcription	Fetal Intestine Large	intestine
47	chr12:58162000-58164800	Strong transcription	Fetal Stomach	stomach
48	chr12:58162000-58164800	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr12:58162200-58164600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:58162200-58164600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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