Variant report

Variant	rs2118138
Chromosome Location	chr12:66698144-66698145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:66697243..66701678-chr12:66713455..66715923,3	K562	blood:
2	chr12:66697262..66699095-chr12:66703905..66706309,2	MCF-7	breast:
3	chr12:66563078..66564680-chr12:66697524..66699997,2	MCF-7	breast:
4	chr12:66684746..66687398-chr12:66696946..66699737,2	MCF-7	breast:
5	chr12:66554922..66556425-chr12:66697932..66699503,2	K562	blood:
6	chr12:66696693..66698195-chr12:66702307..66704926,2	K562	blood:
7	chr12:66696296..66697925-chr12:66698134..66700052,2	MCF-7	breast:
8	chr12:66696640..66699330-chr12:66723248..66725876,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction
ENSG00000127311	Chromatin interaction
ENSG00000222744	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1009211	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10784523	0.99[EUR][1000 genomes]
rs10878401	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10878402	0.96[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10878403	0.96[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs11176125	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176126	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176132	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11610967	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs12146707	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12146757	0.99[EUR][1000 genomes]
rs12146776	0.82[EUR][1000 genomes]
rs12822052	0.98[EUR][1000 genomes]
rs1370125	0.96[EUR][1000 genomes]
rs1921013	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2028095	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2118139	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2118140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904497	0.94[EUR][1000 genomes]
rs3741604	0.89[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3741605	1.00[CEU][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs4430553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6421217	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6581672	0.96[EUR][1000 genomes]
rs7131920	1.00[EUR][1000 genomes]
rs7306114	0.96[EUR][1000 genomes]
rs7308068	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7315366	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7956960	0.85[AFR][1000 genomes]
rs7968129	0.96[EUR][1000 genomes]
rs974349	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2118138	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs2118138	HELB	cis	Nerve Tibial	GTEx
rs2118138	HELB	cis	Muscle Skeletal	GTEx
rs2118138	HELB	cis	cerebellum	SCAN
rs2118138	HELB	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66694800-66698400	Active TSS	Rectal Smooth Muscle	rectum
2	chr12:66695400-66698400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr12:66695800-66698400	Active TSS	Fetal Kidney	kidney
4	chr12:66695800-66698600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:66695800-66698600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
6	chr12:66695800-66698600	Active TSS	Duodenum Mucosa	Duodenum
7	chr12:66695800-66698800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:66695800-66700000	Active TSS	GM12878-XiMat	blood
9	chr12:66696000-66698200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:66696000-66698800	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr12:66696400-66698400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr12:66696400-66698400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr12:66696400-66698400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:66696600-66698800	Flanking Active TSS	Dnd41	blood
15	chr12:66696800-66698800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr12:66696800-66701800	Weak transcription	Left Ventricle	heart
17	chr12:66696800-66702000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:66696800-66702000	Weak transcription	Aorta	Aorta
19	chr12:66696800-66703800	Weak transcription	Lung	lung
20	chr12:66696800-66714800	Weak transcription	NHDF-Ad	bronchial
21	chr12:66696800-66716600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:66696800-66717600	Weak transcription	Fetal Brain Male	brain
23	chr12:66696800-66719600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:66696800-66723600	Weak transcription	HSMM	muscle
25	chr12:66696800-66734200	Weak transcription	HSMMtube	muscle
26	chr12:66697000-66698200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:66697000-66698400	Enhancers	Primary B cells from peripheral blood	blood
28	chr12:66697000-66698400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr12:66697000-66698400	Enhancers	Brain Cingulate Gyrus	brain
30	chr12:66697000-66698400	Enhancers	Fetal Lung	lung
31	chr12:66697000-66698800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:66697000-66698800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr12:66697000-66699000	Enhancers	Brain Angular Gyrus	brain
34	chr12:66697000-66700200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:66697000-66704400	Weak transcription	Brain Germinal Matrix	brain
36	chr12:66697000-66725000	Weak transcription	Ovary	ovary
37	chr12:66697200-66698200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:66697200-66698200	Enhancers	Colon Smooth Muscle	Colon
39	chr12:66697200-66698200	Enhancers	Fetal Brain Female	brain
40	chr12:66697200-66698200	Enhancers	Stomach Mucosa	stomach
41	chr12:66697200-66698400	Enhancers	Brain Substantia Nigra	brain
42	chr12:66697200-66698400	Enhancers	HepG2	liver
43	chr12:66697200-66700600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:66697200-66702000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr12:66697200-66703600	Weak transcription	Spleen	Spleen
46	chr12:66697200-66703800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr12:66697200-66704000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:66697200-66707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:66697200-66716000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr12:66697200-66725600	Weak transcription	Fetal Heart	heart

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