Variant report

Variant	rs2720041
Chromosome Location	chr12:122116393-122116394
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122110522..122113228-chr12:122115462..122118527,3	MCF-7	breast:
2	chr12:122115091..122119007-chr12:122123231..122126528,5	K562	blood:
3	chr12:122114958..122116591-chr12:122123026..122125296,2	K562	blood:

Variant related genes	Relation type
ENSG00000139714	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10770192	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10840612	0.81[AMR][1000 genomes]
rs12320939	0.88[MEX][hapmap]
rs2137434	0.80[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]
rs2458402	0.82[AMR][1000 genomes]
rs2466145	0.80[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]
rs2669166	0.83[MEX][hapmap]
rs2720021	0.81[AMR][1000 genomes]
rs2720022	0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs2942368	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs2942370	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2942379	0.88[MEX][hapmap]
rs2954111	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2954112	0.92[CEU][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3934658	0.84[MEX][hapmap]
rs7297028	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7399127	0.84[MEX][hapmap]
rs7967415	0.92[MEX][hapmap];0.84[TSI][hapmap]
rs925531	0.80[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv527988	chr12:122114593-122116794	Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2720041	PRKAB1	cis	cerebellum	SCAN
rs2720041	RFC5	cis	parietal	SCAN
rs2720041	LRRC43	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122111400-122116400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:122111400-122116800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:122111400-122116800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:122111400-122116800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:122111400-122116800	Weak transcription	Fetal Thymus	thymus
6	chr12:122111400-122117000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:122111400-122117000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:122111400-122117000	Weak transcription	Thymus	Thymus
9	chr12:122111400-122124200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:122111400-122124400	Weak transcription	Brain Anterior Caudate	brain
11	chr12:122111400-122124800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:122111600-122116600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:122111600-122116600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:122111600-122116800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:122111600-122116800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:122111600-122116800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:122111600-122117000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:122111600-122117000	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:122111600-122119800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:122111600-122124600	Weak transcription	Fetal Kidney	kidney
21	chr12:122111800-122117200	Weak transcription	Brain Substantia Nigra	brain
22	chr12:122112800-122116600	Weak transcription	Placenta	Placenta
23	chr12:122113000-122117000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:122114600-122116400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:122114600-122117000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:122116000-122116800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:122116000-122117000	Enhancers	K562	blood
28	chr12:122116000-122117600	Enhancers	Fetal Muscle Leg	muscle
29	chr12:122116200-122117000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:122116200-122117200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:122116200-122117400	Enhancers	Fetal Muscle Trunk	muscle
32	chr12:122116200-122118000	Enhancers	Brain Germinal Matrix	brain

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