Variant report

Variant	rs2118139
Chromosome Location	chr12:66698438-66698439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr12:66696296..66697925-chr12:66698134..66700052,2	MCF-7	breast:
7	chr12:66696640..66699330-chr12:66723248..66725876,2	MCF-7	breast:

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

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1009211	0.95[EUR][1000 genomes]
rs10748038	0.90[CHB][hapmap]
rs10784523	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878401	0.95[EUR][1000 genomes]
rs10878402	0.96[CEU][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs10878403	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176125	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs11176126	0.95[EUR][1000 genomes]
rs11176132	0.95[EUR][1000 genomes]
rs11176138	0.84[AFR][1000 genomes]
rs11610967	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs12146707	0.98[EUR][1000 genomes]
rs12146757	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12146776	0.82[EUR][1000 genomes]
rs12822052	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1370125	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1898305	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1921013	0.96[CEU][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs1971302	0.87[AFR][1000 genomes]
rs2028095	0.93[EUR][1000 genomes]
rs2118138	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2118140	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2904497	0.94[EUR][1000 genomes]
rs3741604	0.89[CEU][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs3741605	1.00[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4430553	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6421217	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs6581672	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7131920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132724	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7133479	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7306114	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308068	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7316880	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7964860	0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7968129	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969887	0.91[CHB][hapmap]
rs7978354	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs974349	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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
rs2118139	HELB	cis	cerebellum	SCAN
rs2118139	HELB	cis	parietal	SCAN
rs2118139	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs2118139	HELB	cis	Nerve Tibial	GTEx
rs2118139	HELB	cis	Muscle Skeletal	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66695800-66698600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:66695800-66698600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
3	chr12:66695800-66698600	Active TSS	Duodenum Mucosa	Duodenum
4	chr12:66695800-66698800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:66695800-66700000	Active TSS	GM12878-XiMat	blood
6	chr12:66696000-66698800	Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr12:66696600-66698800	Flanking Active TSS	Dnd41	blood
8	chr12:66696800-66698800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr12:66696800-66701800	Weak transcription	Left Ventricle	heart
10	chr12:66696800-66702000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:66696800-66702000	Weak transcription	Aorta	Aorta
12	chr12:66696800-66703800	Weak transcription	Lung	lung
13	chr12:66696800-66714800	Weak transcription	NHDF-Ad	bronchial
14	chr12:66696800-66716600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:66696800-66717600	Weak transcription	Fetal Brain Male	brain
16	chr12:66696800-66719600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:66696800-66723600	Weak transcription	HSMM	muscle
18	chr12:66696800-66734200	Weak transcription	HSMMtube	muscle
19	chr12:66697000-66698800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:66697000-66698800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr12:66697000-66699000	Enhancers	Brain Angular Gyrus	brain
22	chr12:66697000-66700200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:66697000-66704400	Weak transcription	Brain Germinal Matrix	brain
24	chr12:66697000-66725000	Weak transcription	Ovary	ovary
25	chr12:66697200-66700600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:66697200-66702000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:66697200-66703600	Weak transcription	Spleen	Spleen
28	chr12:66697200-66703800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:66697200-66704000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:66697200-66707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:66697200-66716000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:66697200-66725600	Weak transcription	Fetal Heart	heart
33	chr12:66697200-66733800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:66697200-66734800	Weak transcription	Esophagus	oesophagus
35	chr12:66697200-66735000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:66697200-66742200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr12:66697400-66698600	Flanking Active TSS	K562	blood
38	chr12:66697400-66698800	Active TSS	Primary T cells fromperipheralblood	blood
39	chr12:66697400-66699000	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr12:66697400-66700600	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:66697400-66703800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:66697400-66703800	Weak transcription	Gastric	stomach
43	chr12:66697400-66704000	Weak transcription	Fetal Intestine Small	intestine
44	chr12:66697400-66707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:66697400-66714800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:66697400-66719800	Weak transcription	Psoas Muscle	Psoas
47	chr12:66697400-66724800	Weak transcription	Pancreas	Pancrea
48	chr12:66697400-66732200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:66697400-66732400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr12:66697400-66735000	Weak transcription	Right Ventricle	heart

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